|
0
|
1 inputfile = orig
|
|
|
2 2 x 70 - 70 d
|
|
|
3 outputhat23=1
|
|
|
4 treein = 0
|
|
|
5 compacttree = 0
|
|
|
6 stacksize: 8192 kb
|
|
|
7 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
8 All-to-all alignment.
|
|
|
9 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
10 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
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|
|
11 1 thread(s)
|
|
|
12
|
|
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13 outputhat23=1
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|
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14 Loading 'hat3.seed' ...
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|
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15 done.
|
|
|
16 Writing hat3 for iterative refinement
|
|
|
17 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
18 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
19 tbutree = 1, compacttree = 0
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|
|
20 Constructing a UPGMA tree ...
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|
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21
0 / 2
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22 done.
|
|
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23
|
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24 Progressive alignment ...
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|
25
STEP 1 /1 (thread 0)
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|
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26 done.
|
|
|
27 tbfast (nuc) Version 7.407
|
|
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28 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
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|
|
29 1 thread(s)
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|
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30
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|
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31 minimumweight = 0.000010
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|
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32 autosubalignment = 0.000000
|
|
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33 nthread = 1
|
|
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34 randomseed = 0
|
|
|
35 blosum 62 / kimura 200
|
|
|
36 poffset = 0
|
|
|
37 niter = 1
|
|
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38 sueff_global = 0.100000
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|
|
39 nadd = 1
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|
40 Loading 'hat3' ... done.
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|
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41 generating a scoring matrix for nucleotide (dist=200) ... done
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42
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43
0 / 2
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44 Segment 1/ 1 1- 72
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45 001-0000-1 (thread 1) identical
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46 Converged.
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47
|
|
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48 Reached 1
|
|
|
49 done
|
|
|
50 dvtditr (nuc) Version 7.407
|
|
|
51 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
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|
|
52 1 thread(s)
|
|
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53
|
|
|
54
|
|
|
55 Strategy:
|
|
|
56 L-INS-i (Probably most accurate, very slow)
|
|
|
57 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
58
|
|
|
59 If unsure which option to use, try 'mafft --auto input > output'.
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|
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60 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
61
|
|
|
62 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
63 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
64 To disable this change, add the --leavegappyregion option.
|
|
|
65
|
|
|
66 inputfile = orig
|
|
|
67 3 x 70 - 70 d
|
|
|
68 nadd = 1
|
|
|
69 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
70
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
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71 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
72 1 thread(s)
|
|
|
73
|
|
|
74 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
75 All-to-all alignment.
|
|
|
76
|
|
|
77
|
|
|
78 ##### writing hat3
|
|
|
79 pairlocalalign (nuc) Version 7.407
|
|
|
80 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
81 1 thread(s)
|
|
|
82
|
|
|
83 nadd = 1
|
|
|
84 ppenalty_ex = -10
|
|
|
85 nthread = 1
|
|
|
86 blosum 62 / kimura 200
|
|
|
87 sueff_global = 0.100000
|
|
|
88 norg = 2
|
|
|
89 njobc = 3
|
|
|
90 Loading 'hat3' ...
|
|
|
91 done.
|
|
|
92 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
93 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
94 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
95
0 / 1 (thread 0)
c
|
|
|
96
|
|
|
97 Combining ..
|
|
|
98 0 / 1
0 / 1
done.
|
|
|
99
|
|
|
100
done.
|
|
|
101
|
|
|
102 addsingle (nuc) Version 7.407
|
|
|
103 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
104 1 thread(s)
|
|
|
105
|
|
|
106
|
|
|
107 Strategy:
|
|
|
108 Multi-INS-fragment (Not tested.)
|
|
|
109 ?
|
|
|
110
|
|
|
111 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
112 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
113
|
|
|
114 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
115 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
116 To disable this change, add the --leavegappyregion option.
|
|
|
117
|
|
|
118 inputfile = orig
|
|
|
119 4 x 83 - 70 d
|
|
|
120 nadd = 1
|
|
|
121 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
122
0 / 3 (thread 0)dndpre (nuc) Version 7.407
|
|
|
123 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
124 1 thread(s)
|
|
|
125
|
|
|
126 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
127 All-to-all alignment.
|
|
|
128
|
|
|
129
|
|
|
130 ##### writing hat3
|
|
|
131 pairlocalalign (nuc) Version 7.407
|
|
|
132 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
133 1 thread(s)
|
|
|
134
|
|
|
135 nadd = 1
|
|
|
136 ppenalty_ex = -10
|
|
|
137 nthread = 1
|
|
|
138 blosum 62 / kimura 200
|
|
|
139 sueff_global = 0.100000
|
|
|
140 norg = 3
|
|
|
141 njobc = 4
|
|
|
142 Loading 'hat3' ...
|
|
|
143 done.
|
|
|
144 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
145 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
146 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
147
0 / 1 (thread 0)
c
|
|
|
148
|
|
|
149 Combining ..
|
|
|
150 0 / 1
0 / 1
done.
|
|
|
151
|
|
|
152
done.
|
|
|
153
|
|
|
154 addsingle (nuc) Version 7.407
|
|
|
155 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
156 1 thread(s)
|
|
|
157
|
|
|
158
|
|
|
159 Strategy:
|
|
|
160 Multi-INS-fragment (Not tested.)
|
|
|
161 ?
|
|
|
162
|
|
|
163 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
164 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
165
|
|
|
166 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
167 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
168 To disable this change, add the --leavegappyregion option.
|
|
|
169
|
|
|
170 inputfile = orig
|
|
|
171 2 x 70 - 70 d
|
|
|
172 outputhat23=1
|
|
|
173 treein = 0
|
|
|
174 compacttree = 0
|
|
|
175 stacksize: 8192 kb
|
|
|
176 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
177 All-to-all alignment.
|
|
|
178 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
179 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
180 1 thread(s)
|
|
|
181
|
|
|
182 outputhat23=1
|
|
|
183 Loading 'hat3.seed' ...
|
|
|
184 done.
|
|
|
185 Writing hat3 for iterative refinement
|
|
|
186 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
187 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
188 tbutree = 1, compacttree = 0
|
|
|
189 Constructing a UPGMA tree ...
|
|
|
190
0 / 2
|
|
|
191 done.
|
|
|
192
|
|
|
193 Progressive alignment ...
|
|
|
194
STEP 1 /1 (thread 0)
|
|
|
195 done.
|
|
|
196 tbfast (nuc) Version 7.407
|
|
|
197 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
198 1 thread(s)
|
|
|
199
|
|
|
200 minimumweight = 0.000010
|
|
|
201 autosubalignment = 0.000000
|
|
|
202 nthread = 1
|
|
|
203 randomseed = 0
|
|
|
204 blosum 62 / kimura 200
|
|
|
205 poffset = 0
|
|
|
206 niter = 1
|
|
|
207 sueff_global = 0.100000
|
|
|
208 nadd = 1
|
|
|
209 Loading 'hat3' ... done.
|
|
|
210 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
211
|
|
|
212
0 / 2
|
|
|
213 Segment 1/ 1 1- 91
|
|
|
214 001-0000-1 (thread 1) identical
|
|
|
215 Converged.
|
|
|
216
|
|
|
217 Reached 1
|
|
|
218 done
|
|
|
219 dvtditr (nuc) Version 7.407
|
|
|
220 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
221 1 thread(s)
|
|
|
222
|
|
|
223
|
|
|
224 Strategy:
|
|
|
225 L-INS-i (Probably most accurate, very slow)
|
|
|
226 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
227
|
|
|
228 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
229 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
230
|
|
|
231 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
232 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
233 To disable this change, add the --leavegappyregion option.
|
|
|
234
|
|
|
235 inputfile = orig
|
|
|
236 2 x 70 - 70 d
|
|
|
237 outputhat23=1
|
|
|
238 treein = 0
|
|
|
239 compacttree = 0
|
|
|
240 stacksize: 8192 kb
|
|
|
241 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
242 All-to-all alignment.
|
|
|
243 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
244 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
245 1 thread(s)
|
|
|
246
|
|
|
247 outputhat23=1
|
|
|
248 Loading 'hat3.seed' ...
|
|
|
249 done.
|
|
|
250 Writing hat3 for iterative refinement
|
|
|
251 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
252 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
253 tbutree = 1, compacttree = 0
|
|
|
254 Constructing a UPGMA tree ...
|
|
|
255
0 / 2
|
|
|
256 done.
|
|
|
257
|
|
|
258 Progressive alignment ...
|
|
|
259
STEP 1 /1 (thread 0)
|
|
|
260 done.
|
|
|
261 tbfast (nuc) Version 7.407
|
|
|
262 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
263 1 thread(s)
|
|
|
264
|
|
|
265 minimumweight = 0.000010
|
|
|
266 autosubalignment = 0.000000
|
|
|
267 nthread = 1
|
|
|
268 randomseed = 0
|
|
|
269 blosum 62 / kimura 200
|
|
|
270 poffset = 0
|
|
|
271 niter = 1
|
|
|
272 sueff_global = 0.100000
|
|
|
273 nadd = 1
|
|
|
274 Loading 'hat3' ... done.
|
|
|
275 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
276
|
|
|
277
0 / 2
|
|
|
278 Segment 1/ 1 1- 108
|
|
|
279 001-0000-1 (thread 1) identical
|
|
|
280 Converged.
|
|
|
281
|
|
|
282 Reached 1
|
|
|
283 done
|
|
|
284 dvtditr (nuc) Version 7.407
|
|
|
285 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
286 1 thread(s)
|
|
|
287
|
|
|
288
|
|
|
289 Strategy:
|
|
|
290 L-INS-i (Probably most accurate, very slow)
|
|
|
291 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
292
|
|
|
293 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
294 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
295
|
|
|
296 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
297 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
298 To disable this change, add the --leavegappyregion option.
|
|
|
299
|
|
|
300 inputfile = orig
|
|
|
301 2 x 70 - 70 d
|
|
|
302 outputhat23=1
|
|
|
303 treein = 0
|
|
|
304 compacttree = 0
|
|
|
305 stacksize: 8192 kb
|
|
|
306 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
307 All-to-all alignment.
|
|
|
308 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
309 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
310 1 thread(s)
|
|
|
311
|
|
|
312 outputhat23=1
|
|
|
313 Loading 'hat3.seed' ...
|
|
|
314 done.
|
|
|
315 Writing hat3 for iterative refinement
|
|
|
316 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
317 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
318 tbutree = 1, compacttree = 0
|
|
|
319 Constructing a UPGMA tree ...
|
|
|
320
0 / 2
|
|
|
321 done.
|
|
|
322
|
|
|
323 Progressive alignment ...
|
|
|
324
STEP 1 /1 (thread 0)
|
|
|
325 done.
|
|
|
326 tbfast (nuc) Version 7.407
|
|
|
327 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
328 1 thread(s)
|
|
|
329
|
|
|
330 minimumweight = 0.000010
|
|
|
331 autosubalignment = 0.000000
|
|
|
332 nthread = 1
|
|
|
333 randomseed = 0
|
|
|
334 blosum 62 / kimura 200
|
|
|
335 poffset = 0
|
|
|
336 niter = 1
|
|
|
337 sueff_global = 0.100000
|
|
|
338 nadd = 1
|
|
|
339 Loading 'hat3' ... done.
|
|
|
340 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
341
|
|
|
342
0 / 2
|
|
|
343 Segment 1/ 1 1- 92
|
|
|
344 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
345 Reached 1
|
|
|
346 done
|
|
|
347 dvtditr (nuc) Version 7.407
|
|
|
348 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
349 1 thread(s)
|
|
|
350
|
|
|
351
|
|
|
352 Strategy:
|
|
|
353 L-INS-i (Probably most accurate, very slow)
|
|
|
354 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
355
|
|
|
356 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
357 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
358
|
|
|
359 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
360 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
361 To disable this change, add the --leavegappyregion option.
|
|
|
362
|
|
|
363 inputfile = orig
|
|
|
364 3 x 76 - 70 d
|
|
|
365 nadd = 1
|
|
|
366 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
367
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
368 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
369 1 thread(s)
|
|
|
370
|
|
|
371 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
372 All-to-all alignment.
|
|
|
373
|
|
|
374
|
|
|
375 ##### writing hat3
|
|
|
376 pairlocalalign (nuc) Version 7.407
|
|
|
377 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
378 1 thread(s)
|
|
|
379
|
|
|
380 nadd = 1
|
|
|
381 ppenalty_ex = -10
|
|
|
382 nthread = 1
|
|
|
383 blosum 62 / kimura 200
|
|
|
384 sueff_global = 0.100000
|
|
|
385 norg = 2
|
|
|
386 njobc = 3
|
|
|
387 Loading 'hat3' ...
|
|
|
388 done.
|
|
|
389 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
390 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
391 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
392
0 / 1 (thread 0)
c
|
|
|
393
|
|
|
394 Combining ..
|
|
|
395 0 / 1
0 / 1
done.
|
|
|
396
|
|
|
397
done.
|
|
|
398
|
|
|
399 addsingle (nuc) Version 7.407
|
|
|
400 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
401 1 thread(s)
|
|
|
402
|
|
|
403
|
|
|
404 Strategy:
|
|
|
405 Multi-INS-fragment (Not tested.)
|
|
|
406 ?
|
|
|
407
|
|
|
408 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
409 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
410
|
|
|
411 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
412 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
413 To disable this change, add the --leavegappyregion option.
|
|
|
414
|
|
|
415 inputfile = orig
|
|
|
416 2 x 70 - 70 d
|
|
|
417 outputhat23=1
|
|
|
418 treein = 0
|
|
|
419 compacttree = 0
|
|
|
420 stacksize: 8192 kb
|
|
|
421 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
422 All-to-all alignment.
|
|
|
423 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
424 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
425 1 thread(s)
|
|
|
426
|
|
|
427 outputhat23=1
|
|
|
428 Loading 'hat3.seed' ...
|
|
|
429 done.
|
|
|
430 Writing hat3 for iterative refinement
|
|
|
431 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
432 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
433 tbutree = 1, compacttree = 0
|
|
|
434 Constructing a UPGMA tree ...
|
|
|
435
0 / 2
|
|
|
436 done.
|
|
|
437
|
|
|
438 Progressive alignment ...
|
|
|
439
STEP 1 /1 (thread 0)
|
|
|
440 done.
|
|
|
441 tbfast (nuc) Version 7.407
|
|
|
442 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
443 1 thread(s)
|
|
|
444
|
|
|
445 minimumweight = 0.000010
|
|
|
446 autosubalignment = 0.000000
|
|
|
447 nthread = 1
|
|
|
448 randomseed = 0
|
|
|
449 blosum 62 / kimura 200
|
|
|
450 poffset = 0
|
|
|
451 niter = 1
|
|
|
452 sueff_global = 0.100000
|
|
|
453 nadd = 1
|
|
|
454 Loading 'hat3' ... done.
|
|
|
455 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
456
|
|
|
457
0 / 2
|
|
|
458 Segment 1/ 1 1- 118
|
|
|
459 001-0000-1 (thread 1) identical
|
|
|
460 Converged.
|
|
|
461
|
|
|
462 Reached 1
|
|
|
463 done
|
|
|
464 dvtditr (nuc) Version 7.407
|
|
|
465 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
466 1 thread(s)
|
|
|
467
|
|
|
468
|
|
|
469 Strategy:
|
|
|
470 L-INS-i (Probably most accurate, very slow)
|
|
|
471 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
472
|
|
|
473 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
474 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
475
|
|
|
476 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
477 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
478 To disable this change, add the --leavegappyregion option.
|
|
|
479
|
|
|
480 inputfile = orig
|
|
|
481 2 x 70 - 70 d
|
|
|
482 outputhat23=1
|
|
|
483 treein = 0
|
|
|
484 compacttree = 0
|
|
|
485 stacksize: 8192 kb
|
|
|
486 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
487 All-to-all alignment.
|
|
|
488 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
489 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
490 1 thread(s)
|
|
|
491
|
|
|
492 outputhat23=1
|
|
|
493 Loading 'hat3.seed' ...
|
|
|
494 done.
|
|
|
495 Writing hat3 for iterative refinement
|
|
|
496 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
497 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
498 tbutree = 1, compacttree = 0
|
|
|
499 Constructing a UPGMA tree ...
|
|
|
500
0 / 2
|
|
|
501 done.
|
|
|
502
|
|
|
503 Progressive alignment ...
|
|
|
504
STEP 1 /1 (thread 0)
|
|
|
505 done.
|
|
|
506 tbfast (nuc) Version 7.407
|
|
|
507 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
508 1 thread(s)
|
|
|
509
|
|
|
510 minimumweight = 0.000010
|
|
|
511 autosubalignment = 0.000000
|
|
|
512 nthread = 1
|
|
|
513 randomseed = 0
|
|
|
514 blosum 62 / kimura 200
|
|
|
515 poffset = 0
|
|
|
516 niter = 1
|
|
|
517 sueff_global = 0.100000
|
|
|
518 nadd = 1
|
|
|
519 Loading 'hat3' ... done.
|
|
|
520 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
521
|
|
|
522
0 / 2
|
|
|
523 Segment 1/ 1 1- 115
|
|
|
524 001-0000-1 (thread 1) identical
|
|
|
525 Converged.
|
|
|
526
|
|
|
527 Reached 1
|
|
|
528 done
|
|
|
529 dvtditr (nuc) Version 7.407
|
|
|
530 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
531 1 thread(s)
|
|
|
532
|
|
|
533
|
|
|
534 Strategy:
|
|
|
535 L-INS-i (Probably most accurate, very slow)
|
|
|
536 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
537
|
|
|
538 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
539 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
540
|
|
|
541 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
542 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
543 To disable this change, add the --leavegappyregion option.
|
|
|
544
|
|
|
545 inputfile = orig
|
|
|
546 2 x 70 - 70 d
|
|
|
547 outputhat23=1
|
|
|
548 treein = 0
|
|
|
549 compacttree = 0
|
|
|
550 stacksize: 8192 kb
|
|
|
551 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
552 All-to-all alignment.
|
|
|
553 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
554 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
555 1 thread(s)
|
|
|
556
|
|
|
557 outputhat23=1
|
|
|
558 Loading 'hat3.seed' ...
|
|
|
559 done.
|
|
|
560 Writing hat3 for iterative refinement
|
|
|
561 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
562 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
563 tbutree = 1, compacttree = 0
|
|
|
564 Constructing a UPGMA tree ...
|
|
|
565
0 / 2
|
|
|
566 done.
|
|
|
567
|
|
|
568 Progressive alignment ...
|
|
|
569
STEP 1 /1 (thread 0)
|
|
|
570 done.
|
|
|
571 tbfast (nuc) Version 7.407
|
|
|
572 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
573 1 thread(s)
|
|
|
574
|
|
|
575 minimumweight = 0.000010
|
|
|
576 autosubalignment = 0.000000
|
|
|
577 nthread = 1
|
|
|
578 randomseed = 0
|
|
|
579 blosum 62 / kimura 200
|
|
|
580 poffset = 0
|
|
|
581 niter = 1
|
|
|
582 sueff_global = 0.100000
|
|
|
583 nadd = 1
|
|
|
584 Loading 'hat3' ... done.
|
|
|
585 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
586
|
|
|
587
0 / 2
|
|
|
588 Segment 1/ 1 1- 94
|
|
|
589 001-0000-1 (thread 1) identical
|
|
|
590 Converged.
|
|
|
591
|
|
|
592 Reached 1
|
|
|
593 done
|
|
|
594 dvtditr (nuc) Version 7.407
|
|
|
595 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
596 1 thread(s)
|
|
|
597
|
|
|
598
|
|
|
599 Strategy:
|
|
|
600 L-INS-i (Probably most accurate, very slow)
|
|
|
601 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
602
|
|
|
603 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
604 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
605
|
|
|
606 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
607 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
608 To disable this change, add the --leavegappyregion option.
|
|
|
609
|
|
|
610 inputfile = orig
|
|
|
611 2 x 70 - 70 d
|
|
|
612 outputhat23=1
|
|
|
613 treein = 0
|
|
|
614 compacttree = 0
|
|
|
615 stacksize: 8192 kb
|
|
|
616 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
617 All-to-all alignment.
|
|
|
618 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
619 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
620 1 thread(s)
|
|
|
621
|
|
|
622 outputhat23=1
|
|
|
623 Loading 'hat3.seed' ...
|
|
|
624 done.
|
|
|
625 Writing hat3 for iterative refinement
|
|
|
626 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
627 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
628 tbutree = 1, compacttree = 0
|
|
|
629 Constructing a UPGMA tree ...
|
|
|
630
0 / 2
|
|
|
631 done.
|
|
|
632
|
|
|
633 Progressive alignment ...
|
|
|
634
STEP 1 /1 (thread 0)
|
|
|
635 done.
|
|
|
636 tbfast (nuc) Version 7.407
|
|
|
637 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
638 1 thread(s)
|
|
|
639
|
|
|
640 minimumweight = 0.000010
|
|
|
641 autosubalignment = 0.000000
|
|
|
642 nthread = 1
|
|
|
643 randomseed = 0
|
|
|
644 blosum 62 / kimura 200
|
|
|
645 poffset = 0
|
|
|
646 niter = 1
|
|
|
647 sueff_global = 0.100000
|
|
|
648 nadd = 1
|
|
|
649 Loading 'hat3' ... done.
|
|
|
650 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
651
|
|
|
652
0 / 2
|
|
|
653 Segment 1/ 1 1- 87
|
|
|
654 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
655 Reached 1
|
|
|
656 done
|
|
|
657 dvtditr (nuc) Version 7.407
|
|
|
658 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
659 1 thread(s)
|
|
|
660
|
|
|
661
|
|
|
662 Strategy:
|
|
|
663 L-INS-i (Probably most accurate, very slow)
|
|
|
664 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
665
|
|
|
666 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
667 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
668
|
|
|
669 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
670 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
671 To disable this change, add the --leavegappyregion option.
|
|
|
672
|
|
|
673 inputfile = orig
|
|
|
674 3 x 80 - 70 d
|
|
|
675 nadd = 1
|
|
|
676 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
677
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
678 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
679 1 thread(s)
|
|
|
680
|
|
|
681 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
682 All-to-all alignment.
|
|
|
683
|
|
|
684
|
|
|
685 ##### writing hat3
|
|
|
686 pairlocalalign (nuc) Version 7.407
|
|
|
687 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
688 1 thread(s)
|
|
|
689
|
|
|
690 nadd = 1
|
|
|
691 ppenalty_ex = -10
|
|
|
692 nthread = 1
|
|
|
693 blosum 62 / kimura 200
|
|
|
694 sueff_global = 0.100000
|
|
|
695 norg = 2
|
|
|
696 njobc = 3
|
|
|
697 Loading 'hat3' ...
|
|
|
698 done.
|
|
|
699 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
700 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
701 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
702
0 / 1 (thread 0)
c
|
|
|
703
|
|
|
704 Combining ..
|
|
|
705 0 / 1
0 / 1
done.
|
|
|
706
|
|
|
707
done.
|
|
|
708
|
|
|
709 addsingle (nuc) Version 7.407
|
|
|
710 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
711 1 thread(s)
|
|
|
712
|
|
|
713
|
|
|
714 Strategy:
|
|
|
715 Multi-INS-fragment (Not tested.)
|
|
|
716 ?
|
|
|
717
|
|
|
718 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
719 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
720
|
|
|
721 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
722 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
723 To disable this change, add the --leavegappyregion option.
|
|
|
724
|
|
|
725 inputfile = orig
|
|
|
726 3 x 84 - 70 d
|
|
|
727 nadd = 1
|
|
|
728 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
729
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
730 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
731 1 thread(s)
|
|
|
732
|
|
|
733 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
734 All-to-all alignment.
|
|
|
735
|
|
|
736
|
|
|
737 ##### writing hat3
|
|
|
738 pairlocalalign (nuc) Version 7.407
|
|
|
739 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
740 1 thread(s)
|
|
|
741
|
|
|
742 nadd = 1
|
|
|
743 ppenalty_ex = -10
|
|
|
744 nthread = 1
|
|
|
745 blosum 62 / kimura 200
|
|
|
746 sueff_global = 0.100000
|
|
|
747 norg = 2
|
|
|
748 njobc = 3
|
|
|
749 Loading 'hat3' ...
|
|
|
750 done.
|
|
|
751 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
752 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
753 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
754
0 / 1 (thread 0)
c
|
|
|
755
|
|
|
756 Combining ..
|
|
|
757 0 / 1
0 / 1
done.
|
|
|
758
|
|
|
759
done.
|
|
|
760
|
|
|
761 addsingle (nuc) Version 7.407
|
|
|
762 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
763 1 thread(s)
|
|
|
764
|
|
|
765
|
|
|
766 Strategy:
|
|
|
767 Multi-INS-fragment (Not tested.)
|
|
|
768 ?
|
|
|
769
|
|
|
770 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
771 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
772
|
|
|
773 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
774 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
775 To disable this change, add the --leavegappyregion option.
|
|
|
776
|
|
|
777 inputfile = orig
|
|
|
778 4 x 82 - 75 d
|
|
|
779 nthread = 1
|
|
|
780 nthreadpair = 1
|
|
|
781 nthreadtb = 1
|
|
|
782 ppenalty_ex = 0
|
|
|
783 stacksize: 8192 kb
|
|
|
784 nsubalignments = 2
|
|
|
785 maxmem = 2
|
|
|
786 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
787 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
788
|
|
|
789
|
|
|
790
|
|
|
791 Making a distance matrix ..
|
|
|
792
1 / 4 (thread 0)
|
|
|
793 done.
|
|
|
794
|
|
|
795 Constructing a UPGMA tree ...
|
|
|
796
|
|
|
797
0 / 4
|
|
|
798 done.
|
|
|
799
|
|
|
800 Checking subalignment 1:
|
|
|
801 -> OK
|
|
|
802 Checking subalignment 2:
|
|
|
803 -> OK
|
|
|
804 Progressive alignment 1/2...
|
|
|
805
STEP 3 / 3 (thread 0) f
|
|
|
806 done.
|
|
|
807
|
|
|
808 Making a distance matrix from msa..
|
|
|
809
0 / 4 (thread 0)
|
|
|
810 done.
|
|
|
811
|
|
|
812 Constructing a UPGMA tree ...
|
|
|
813
|
|
|
814
0 / 4
|
|
|
815 done.
|
|
|
816
|
|
|
817 Checking subalignment 1:
|
|
|
818 -> OK
|
|
|
819 Checking subalignment 2:
|
|
|
820 -> OK
|
|
|
821 Progressive alignment 2/2...
|
|
|
822
STEP 3 / 3 (thread 0) f
|
|
|
823 done.
|
|
|
824
|
|
|
825 disttbfast (nuc) Version 7.407
|
|
|
826 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
827 1 thread(s)
|
|
|
828
|
|
|
829 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
830
0 / 4 (thread 0)dndpre (nuc) Version 7.407
|
|
|
831 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
832 1 thread(s)
|
|
|
833
|
|
|
834 minimumweight = 0.000010
|
|
|
835 autosubalignment = 0.000000
|
|
|
836 nthread = 1
|
|
|
837 randomseed = 0
|
|
|
838 blosum 62 / kimura 200
|
|
|
839 poffset = 0
|
|
|
840 niter = 1
|
|
|
841 sueff_global = 0.100000
|
|
|
842 nadd = 1
|
|
|
843 nsubalignments = 2
|
|
|
844 maxmem = 2
|
|
|
845 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
846
|
|
|
847
|
|
|
848
0 / 4
|
|
|
849
|
|
|
850 Checking subalignment 1:
|
|
|
851 1 2
|
|
|
852 -> OK
|
|
|
853
|
|
|
854 Checking subalignment 2:
|
|
|
855 3 4
|
|
|
856 -> OK
|
|
|
857 Segment 1/ 1 1- 91
|
|
|
858 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-1 (thread 1) identical
001-0004-1 (thread 1) better
|
|
|
859 Reached 1
|
|
|
860 done
|
|
|
861 dvtditr (nuc) Version 7.407
|
|
|
862 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
863 1 thread(s)
|
|
|
864
|
|
|
865
|
|
|
866 Strategy:
|
|
|
867 FFT-NS-i (Standard)
|
|
|
868 Iterative refinement method (max. 1 iterations)
|
|
|
869
|
|
|
870 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
871 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
872
|
|
|
873 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
874 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
875 To disable this change, add the --leavegappyregion option.
|
|
|
876
|
|
|
877 inputfile = orig
|
|
|
878 2 x 70 - 70 d
|
|
|
879 outputhat23=1
|
|
|
880 treein = 0
|
|
|
881 compacttree = 0
|
|
|
882 stacksize: 8192 kb
|
|
|
883 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
884 All-to-all alignment.
|
|
|
885 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
886 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
887 1 thread(s)
|
|
|
888
|
|
|
889 outputhat23=1
|
|
|
890 Loading 'hat3.seed' ...
|
|
|
891 done.
|
|
|
892 Writing hat3 for iterative refinement
|
|
|
893 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
894 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
895 tbutree = 1, compacttree = 0
|
|
|
896 Constructing a UPGMA tree ...
|
|
|
897
0 / 2
|
|
|
898 done.
|
|
|
899
|
|
|
900 Progressive alignment ...
|
|
|
901
STEP 1 /1 (thread 0)
|
|
|
902 done.
|
|
|
903 tbfast (nuc) Version 7.407
|
|
|
904 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
905 1 thread(s)
|
|
|
906
|
|
|
907 minimumweight = 0.000010
|
|
|
908 autosubalignment = 0.000000
|
|
|
909 nthread = 1
|
|
|
910 randomseed = 0
|
|
|
911 blosum 62 / kimura 200
|
|
|
912 poffset = 0
|
|
|
913 niter = 1
|
|
|
914 sueff_global = 0.100000
|
|
|
915 nadd = 1
|
|
|
916 Loading 'hat3' ... done.
|
|
|
917 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
918
|
|
|
919
0 / 2
|
|
|
920 Segment 1/ 1 1- 78
|
|
|
921 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
922 Reached 1
|
|
|
923 done
|
|
|
924 dvtditr (nuc) Version 7.407
|
|
|
925 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
926 1 thread(s)
|
|
|
927
|
|
|
928
|
|
|
929 Strategy:
|
|
|
930 L-INS-i (Probably most accurate, very slow)
|
|
|
931 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
932
|
|
|
933 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
934 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
935
|
|
|
936 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
937 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
938 To disable this change, add the --leavegappyregion option.
|
|
|
939
|
|
|
940 inputfile = orig
|
|
|
941 2 x 70 - 70 d
|
|
|
942 outputhat23=1
|
|
|
943 treein = 0
|
|
|
944 compacttree = 0
|
|
|
945 stacksize: 8192 kb
|
|
|
946 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
947 All-to-all alignment.
|
|
|
948 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
949 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
950 1 thread(s)
|
|
|
951
|
|
|
952 outputhat23=1
|
|
|
953 Loading 'hat3.seed' ...
|
|
|
954 done.
|
|
|
955 Writing hat3 for iterative refinement
|
|
|
956 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
957 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
958 tbutree = 1, compacttree = 0
|
|
|
959 Constructing a UPGMA tree ...
|
|
|
960
0 / 2
|
|
|
961 done.
|
|
|
962
|
|
|
963 Progressive alignment ...
|
|
|
964
STEP 1 /1 (thread 0)
|
|
|
965 done.
|
|
|
966 tbfast (nuc) Version 7.407
|
|
|
967 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
968 1 thread(s)
|
|
|
969
|
|
|
970 minimumweight = 0.000010
|
|
|
971 autosubalignment = 0.000000
|
|
|
972 nthread = 1
|
|
|
973 randomseed = 0
|
|
|
974 blosum 62 / kimura 200
|
|
|
975 poffset = 0
|
|
|
976 niter = 1
|
|
|
977 sueff_global = 0.100000
|
|
|
978 nadd = 1
|
|
|
979 Loading 'hat3' ... done.
|
|
|
980 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
981
|
|
|
982
0 / 2
|
|
|
983 Segment 1/ 1 1- 73
|
|
|
984 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
985 Reached 1
|
|
|
986 done
|
|
|
987 dvtditr (nuc) Version 7.407
|
|
|
988 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
989 1 thread(s)
|
|
|
990
|
|
|
991
|
|
|
992 Strategy:
|
|
|
993 L-INS-i (Probably most accurate, very slow)
|
|
|
994 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
995
|
|
|
996 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
997 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
998
|
|
|
999 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1000 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1001 To disable this change, add the --leavegappyregion option.
|
|
|
1002
|
|
|
1003 inputfile = orig
|
|
|
1004 2 x 70 - 70 d
|
|
|
1005 outputhat23=1
|
|
|
1006 treein = 0
|
|
|
1007 compacttree = 0
|
|
|
1008 stacksize: 8192 kb
|
|
|
1009 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1010 All-to-all alignment.
|
|
|
1011 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1012 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1013 1 thread(s)
|
|
|
1014
|
|
|
1015 outputhat23=1
|
|
|
1016 Loading 'hat3.seed' ...
|
|
|
1017 done.
|
|
|
1018 Writing hat3 for iterative refinement
|
|
|
1019 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1020 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1021 tbutree = 1, compacttree = 0
|
|
|
1022 Constructing a UPGMA tree ...
|
|
|
1023
0 / 2
|
|
|
1024 done.
|
|
|
1025
|
|
|
1026 Progressive alignment ...
|
|
|
1027
STEP 1 /1 (thread 0)
|
|
|
1028 done.
|
|
|
1029 tbfast (nuc) Version 7.407
|
|
|
1030 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1031 1 thread(s)
|
|
|
1032
|
|
|
1033 minimumweight = 0.000010
|
|
|
1034 autosubalignment = 0.000000
|
|
|
1035 nthread = 1
|
|
|
1036 randomseed = 0
|
|
|
1037 blosum 62 / kimura 200
|
|
|
1038 poffset = 0
|
|
|
1039 niter = 1
|
|
|
1040 sueff_global = 0.100000
|
|
|
1041 nadd = 1
|
|
|
1042 Loading 'hat3' ... done.
|
|
|
1043 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1044
|
|
|
1045
0 / 2
|
|
|
1046 Segment 1/ 1 1- 84
|
|
|
1047 001-0000-1 (thread 1) identical
|
|
|
1048 Converged.
|
|
|
1049
|
|
|
1050 Reached 1
|
|
|
1051 done
|
|
|
1052 dvtditr (nuc) Version 7.407
|
|
|
1053 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1054 1 thread(s)
|
|
|
1055
|
|
|
1056
|
|
|
1057 Strategy:
|
|
|
1058 L-INS-i (Probably most accurate, very slow)
|
|
|
1059 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1060
|
|
|
1061 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1062 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1063
|
|
|
1064 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1065 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1066 To disable this change, add the --leavegappyregion option.
|
|
|
1067
|
|
|
1068 inputfile = orig
|
|
|
1069 2 x 70 - 70 d
|
|
|
1070 outputhat23=1
|
|
|
1071 treein = 0
|
|
|
1072 compacttree = 0
|
|
|
1073 stacksize: 8192 kb
|
|
|
1074 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1075 All-to-all alignment.
|
|
|
1076 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1077 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1078 1 thread(s)
|
|
|
1079
|
|
|
1080 outputhat23=1
|
|
|
1081 Loading 'hat3.seed' ...
|
|
|
1082 done.
|
|
|
1083 Writing hat3 for iterative refinement
|
|
|
1084 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1085 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1086 tbutree = 1, compacttree = 0
|
|
|
1087 Constructing a UPGMA tree ...
|
|
|
1088
0 / 2
|
|
|
1089 done.
|
|
|
1090
|
|
|
1091 Progressive alignment ...
|
|
|
1092
STEP 1 /1 (thread 0)
|
|
|
1093 done.
|
|
|
1094 tbfast (nuc) Version 7.407
|
|
|
1095 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1096 1 thread(s)
|
|
|
1097
|
|
|
1098 minimumweight = 0.000010
|
|
|
1099 autosubalignment = 0.000000
|
|
|
1100 nthread = 1
|
|
|
1101 randomseed = 0
|
|
|
1102 blosum 62 / kimura 200
|
|
|
1103 poffset = 0
|
|
|
1104 niter = 1
|
|
|
1105 sueff_global = 0.100000
|
|
|
1106 nadd = 1
|
|
|
1107 Loading 'hat3' ... done.
|
|
|
1108 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1109
|
|
|
1110
0 / 2
|
|
|
1111 Segment 1/ 1 1- 88
|
|
|
1112 001-0000-1 (thread 1) identical
|
|
|
1113 Converged.
|
|
|
1114
|
|
|
1115 Reached 1
|
|
|
1116 done
|
|
|
1117 dvtditr (nuc) Version 7.407
|
|
|
1118 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1119 1 thread(s)
|
|
|
1120
|
|
|
1121
|
|
|
1122 Strategy:
|
|
|
1123 L-INS-i (Probably most accurate, very slow)
|
|
|
1124 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1125
|
|
|
1126 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1127 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1128
|
|
|
1129 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1130 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1131 To disable this change, add the --leavegappyregion option.
|
|
|
1132
|
|
|
1133 inputfile = orig
|
|
|
1134 2 x 70 - 70 d
|
|
|
1135 outputhat23=1
|
|
|
1136 treein = 0
|
|
|
1137 compacttree = 0
|
|
|
1138 stacksize: 8192 kb
|
|
|
1139 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1140 All-to-all alignment.
|
|
|
1141 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1142 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1143 1 thread(s)
|
|
|
1144
|
|
|
1145 outputhat23=1
|
|
|
1146 Loading 'hat3.seed' ...
|
|
|
1147 done.
|
|
|
1148 Writing hat3 for iterative refinement
|
|
|
1149 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1150 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1151 tbutree = 1, compacttree = 0
|
|
|
1152 Constructing a UPGMA tree ...
|
|
|
1153
0 / 2
|
|
|
1154 done.
|
|
|
1155
|
|
|
1156 Progressive alignment ...
|
|
|
1157
STEP 1 /1 (thread 0)
|
|
|
1158 done.
|
|
|
1159 tbfast (nuc) Version 7.407
|
|
|
1160 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1161 1 thread(s)
|
|
|
1162
|
|
|
1163 minimumweight = 0.000010
|
|
|
1164 autosubalignment = 0.000000
|
|
|
1165 nthread = 1
|
|
|
1166 randomseed = 0
|
|
|
1167 blosum 62 / kimura 200
|
|
|
1168 poffset = 0
|
|
|
1169 niter = 1
|
|
|
1170 sueff_global = 0.100000
|
|
|
1171 nadd = 1
|
|
|
1172 Loading 'hat3' ... done.
|
|
|
1173 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1174
|
|
|
1175
0 / 2
|
|
|
1176 Segment 1/ 1 1- 105
|
|
|
1177 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
1178 Reached 1
|
|
|
1179 done
|
|
|
1180 dvtditr (nuc) Version 7.407
|
|
|
1181 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1182 1 thread(s)
|
|
|
1183
|
|
|
1184
|
|
|
1185 Strategy:
|
|
|
1186 L-INS-i (Probably most accurate, very slow)
|
|
|
1187 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1188
|
|
|
1189 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1190 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1191
|
|
|
1192 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1193 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1194 To disable this change, add the --leavegappyregion option.
|
|
|
1195
|
|
|
1196 inputfile = orig
|
|
|
1197 2 x 70 - 70 d
|
|
|
1198 outputhat23=1
|
|
|
1199 treein = 0
|
|
|
1200 compacttree = 0
|
|
|
1201 stacksize: 8192 kb
|
|
|
1202 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1203 All-to-all alignment.
|
|
|
1204 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1205 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1206 1 thread(s)
|
|
|
1207
|
|
|
1208 outputhat23=1
|
|
|
1209 Loading 'hat3.seed' ...
|
|
|
1210 done.
|
|
|
1211 Writing hat3 for iterative refinement
|
|
|
1212 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1213 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1214 tbutree = 1, compacttree = 0
|
|
|
1215 Constructing a UPGMA tree ...
|
|
|
1216
0 / 2
|
|
|
1217 done.
|
|
|
1218
|
|
|
1219 Progressive alignment ...
|
|
|
1220
STEP 1 /1 (thread 0)
|
|
|
1221 done.
|
|
|
1222 tbfast (nuc) Version 7.407
|
|
|
1223 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1224 1 thread(s)
|
|
|
1225
|
|
|
1226 minimumweight = 0.000010
|
|
|
1227 autosubalignment = 0.000000
|
|
|
1228 nthread = 1
|
|
|
1229 randomseed = 0
|
|
|
1230 blosum 62 / kimura 200
|
|
|
1231 poffset = 0
|
|
|
1232 niter = 1
|
|
|
1233 sueff_global = 0.100000
|
|
|
1234 nadd = 1
|
|
|
1235 Loading 'hat3' ... done.
|
|
|
1236 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1237
|
|
|
1238
0 / 2
|
|
|
1239 Segment 1/ 1 1- 77
|
|
|
1240 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
1241 Reached 1
|
|
|
1242 done
|
|
|
1243 dvtditr (nuc) Version 7.407
|
|
|
1244 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1245 1 thread(s)
|
|
|
1246
|
|
|
1247
|
|
|
1248 Strategy:
|
|
|
1249 L-INS-i (Probably most accurate, very slow)
|
|
|
1250 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1251
|
|
|
1252 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1253 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1254
|
|
|
1255 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1256 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1257 To disable this change, add the --leavegappyregion option.
|
|
|
1258
|
|
|
1259 inputfile = orig
|
|
|
1260 3 x 76 - 70 d
|
|
|
1261 nadd = 1
|
|
|
1262 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1263
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
1264 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1265 1 thread(s)
|
|
|
1266
|
|
|
1267 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1268 All-to-all alignment.
|
|
|
1269
|
|
|
1270
|
|
|
1271 ##### writing hat3
|
|
|
1272 pairlocalalign (nuc) Version 7.407
|
|
|
1273 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1274 1 thread(s)
|
|
|
1275
|
|
|
1276 nadd = 1
|
|
|
1277 ppenalty_ex = -10
|
|
|
1278 nthread = 1
|
|
|
1279 blosum 62 / kimura 200
|
|
|
1280 sueff_global = 0.100000
|
|
|
1281 norg = 2
|
|
|
1282 njobc = 3
|
|
|
1283 Loading 'hat3' ...
|
|
|
1284 done.
|
|
|
1285 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1286 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
1287 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
1288
0 / 1 (thread 0)
c
|
|
|
1289
|
|
|
1290 Combining ..
|
|
|
1291 0 / 1
0 / 1
done.
|
|
|
1292
|
|
|
1293
done.
|
|
|
1294
|
|
|
1295 addsingle (nuc) Version 7.407
|
|
|
1296 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1297 1 thread(s)
|
|
|
1298
|
|
|
1299
|
|
|
1300 Strategy:
|
|
|
1301 Multi-INS-fragment (Not tested.)
|
|
|
1302 ?
|
|
|
1303
|
|
|
1304 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1305 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1306
|
|
|
1307 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1308 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1309 To disable this change, add the --leavegappyregion option.
|
|
|
1310
|
|
|
1311 inputfile = orig
|
|
|
1312 3 x 79 - 70 d
|
|
|
1313 nadd = 1
|
|
|
1314 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1315
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
1316 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1317 1 thread(s)
|
|
|
1318
|
|
|
1319 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1320 All-to-all alignment.
|
|
|
1321
|
|
|
1322
|
|
|
1323 ##### writing hat3
|
|
|
1324 pairlocalalign (nuc) Version 7.407
|
|
|
1325 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1326 1 thread(s)
|
|
|
1327
|
|
|
1328 nadd = 1
|
|
|
1329 ppenalty_ex = -10
|
|
|
1330 nthread = 1
|
|
|
1331 blosum 62 / kimura 200
|
|
|
1332 sueff_global = 0.100000
|
|
|
1333 norg = 2
|
|
|
1334 njobc = 3
|
|
|
1335 Loading 'hat3' ...
|
|
|
1336 done.
|
|
|
1337 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1338 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
1339 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
1340
0 / 1 (thread 0)
c
|
|
|
1341
|
|
|
1342 Combining ..
|
|
|
1343 0 / 1
0 / 1
done.
|
|
|
1344
|
|
|
1345
done.
|
|
|
1346
|
|
|
1347 addsingle (nuc) Version 7.407
|
|
|
1348 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1349 1 thread(s)
|
|
|
1350
|
|
|
1351
|
|
|
1352 Strategy:
|
|
|
1353 Multi-INS-fragment (Not tested.)
|
|
|
1354 ?
|
|
|
1355
|
|
|
1356 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1357 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1358
|
|
|
1359 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1360 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1361 To disable this change, add the --leavegappyregion option.
|
|
|
1362
|
|
|
1363 inputfile = orig
|
|
|
1364 3 x 80 - 70 d
|
|
|
1365 nadd = 1
|
|
|
1366 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1367
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
1368 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1369 1 thread(s)
|
|
|
1370
|
|
|
1371 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1372 All-to-all alignment.
|
|
|
1373
|
|
|
1374
|
|
|
1375 ##### writing hat3
|
|
|
1376 pairlocalalign (nuc) Version 7.407
|
|
|
1377 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1378 1 thread(s)
|
|
|
1379
|
|
|
1380 nadd = 1
|
|
|
1381 ppenalty_ex = -10
|
|
|
1382 nthread = 1
|
|
|
1383 blosum 62 / kimura 200
|
|
|
1384 sueff_global = 0.100000
|
|
|
1385 norg = 2
|
|
|
1386 njobc = 3
|
|
|
1387 Loading 'hat3' ...
|
|
|
1388 done.
|
|
|
1389 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1390 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
1391 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
1392
0 / 1 (thread 0)
c
|
|
|
1393
|
|
|
1394 Combining ..
|
|
|
1395 0 / 1
0 / 1
done.
|
|
|
1396
|
|
|
1397
done.
|
|
|
1398
|
|
|
1399 addsingle (nuc) Version 7.407
|
|
|
1400 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1401 1 thread(s)
|
|
|
1402
|
|
|
1403
|
|
|
1404 Strategy:
|
|
|
1405 Multi-INS-fragment (Not tested.)
|
|
|
1406 ?
|
|
|
1407
|
|
|
1408 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1409 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1410
|
|
|
1411 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1412 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1413 To disable this change, add the --leavegappyregion option.
|
|
|
1414
|
|
|
1415 inputfile = orig
|
|
|
1416 2 x 70 - 70 d
|
|
|
1417 outputhat23=1
|
|
|
1418 treein = 0
|
|
|
1419 compacttree = 0
|
|
|
1420 stacksize: 8192 kb
|
|
|
1421 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1422 All-to-all alignment.
|
|
|
1423 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1424 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1425 1 thread(s)
|
|
|
1426
|
|
|
1427 outputhat23=1
|
|
|
1428 Loading 'hat3.seed' ...
|
|
|
1429 done.
|
|
|
1430 Writing hat3 for iterative refinement
|
|
|
1431 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1432 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1433 tbutree = 1, compacttree = 0
|
|
|
1434 Constructing a UPGMA tree ...
|
|
|
1435
0 / 2
|
|
|
1436 done.
|
|
|
1437
|
|
|
1438 Progressive alignment ...
|
|
|
1439
STEP 1 /1 (thread 0)
|
|
|
1440 done.
|
|
|
1441 tbfast (nuc) Version 7.407
|
|
|
1442 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1443 1 thread(s)
|
|
|
1444
|
|
|
1445 minimumweight = 0.000010
|
|
|
1446 autosubalignment = 0.000000
|
|
|
1447 nthread = 1
|
|
|
1448 randomseed = 0
|
|
|
1449 blosum 62 / kimura 200
|
|
|
1450 poffset = 0
|
|
|
1451 niter = 1
|
|
|
1452 sueff_global = 0.100000
|
|
|
1453 nadd = 1
|
|
|
1454 Loading 'hat3' ... done.
|
|
|
1455 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1456
|
|
|
1457
0 / 2
|
|
|
1458 Segment 1/ 1 1- 97
|
|
|
1459 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
1460 Reached 1
|
|
|
1461 done
|
|
|
1462 dvtditr (nuc) Version 7.407
|
|
|
1463 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1464 1 thread(s)
|
|
|
1465
|
|
|
1466
|
|
|
1467 Strategy:
|
|
|
1468 L-INS-i (Probably most accurate, very slow)
|
|
|
1469 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1470
|
|
|
1471 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1472 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1473
|
|
|
1474 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1475 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1476 To disable this change, add the --leavegappyregion option.
|
|
|
1477
|
|
|
1478 inputfile = orig
|
|
|
1479 2 x 70 - 70 d
|
|
|
1480 outputhat23=1
|
|
|
1481 treein = 0
|
|
|
1482 compacttree = 0
|
|
|
1483 stacksize: 8192 kb
|
|
|
1484 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1485 All-to-all alignment.
|
|
|
1486 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1487 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1488 1 thread(s)
|
|
|
1489
|
|
|
1490 outputhat23=1
|
|
|
1491 Loading 'hat3.seed' ...
|
|
|
1492 done.
|
|
|
1493 Writing hat3 for iterative refinement
|
|
|
1494 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1495 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1496 tbutree = 1, compacttree = 0
|
|
|
1497 Constructing a UPGMA tree ...
|
|
|
1498
0 / 2
|
|
|
1499 done.
|
|
|
1500
|
|
|
1501 Progressive alignment ...
|
|
|
1502
STEP 1 /1 (thread 0)
|
|
|
1503 done.
|
|
|
1504 tbfast (nuc) Version 7.407
|
|
|
1505 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1506 1 thread(s)
|
|
|
1507
|
|
|
1508 minimumweight = 0.000010
|
|
|
1509 autosubalignment = 0.000000
|
|
|
1510 nthread = 1
|
|
|
1511 randomseed = 0
|
|
|
1512 blosum 62 / kimura 200
|
|
|
1513 poffset = 0
|
|
|
1514 niter = 1
|
|
|
1515 sueff_global = 0.100000
|
|
|
1516 nadd = 1
|
|
|
1517 Loading 'hat3' ... done.
|
|
|
1518 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1519
|
|
|
1520
0 / 2
|
|
|
1521 Segment 1/ 1 1- 72
|
|
|
1522 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
1523 Reached 1
|
|
|
1524 done
|
|
|
1525 dvtditr (nuc) Version 7.407
|
|
|
1526 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1527 1 thread(s)
|
|
|
1528
|
|
|
1529
|
|
|
1530 Strategy:
|
|
|
1531 L-INS-i (Probably most accurate, very slow)
|
|
|
1532 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1533
|
|
|
1534 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1535 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1536
|
|
|
1537 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1538 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1539 To disable this change, add the --leavegappyregion option.
|
|
|
1540
|
|
|
1541 inputfile = orig
|
|
|
1542 2 x 70 - 70 d
|
|
|
1543 outputhat23=1
|
|
|
1544 treein = 0
|
|
|
1545 compacttree = 0
|
|
|
1546 stacksize: 8192 kb
|
|
|
1547 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1548 All-to-all alignment.
|
|
|
1549 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1550 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1551 1 thread(s)
|
|
|
1552
|
|
|
1553 outputhat23=1
|
|
|
1554 Loading 'hat3.seed' ...
|
|
|
1555 done.
|
|
|
1556 Writing hat3 for iterative refinement
|
|
|
1557 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1558 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1559 tbutree = 1, compacttree = 0
|
|
|
1560 Constructing a UPGMA tree ...
|
|
|
1561
0 / 2
|
|
|
1562 done.
|
|
|
1563
|
|
|
1564 Progressive alignment ...
|
|
|
1565
STEP 1 /1 (thread 0)
|
|
|
1566 done.
|
|
|
1567 tbfast (nuc) Version 7.407
|
|
|
1568 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1569 1 thread(s)
|
|
|
1570
|
|
|
1571 minimumweight = 0.000010
|
|
|
1572 autosubalignment = 0.000000
|
|
|
1573 nthread = 1
|
|
|
1574 randomseed = 0
|
|
|
1575 blosum 62 / kimura 200
|
|
|
1576 poffset = 0
|
|
|
1577 niter = 1
|
|
|
1578 sueff_global = 0.100000
|
|
|
1579 nadd = 1
|
|
|
1580 Loading 'hat3' ... done.
|
|
|
1581 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1582
|
|
|
1583
0 / 2
|
|
|
1584 Segment 1/ 1 1- 97
|
|
|
1585 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
|
|
|
1586 Reached 1
|
|
|
1587 done
|
|
|
1588 dvtditr (nuc) Version 7.407
|
|
|
1589 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1590 1 thread(s)
|
|
|
1591
|
|
|
1592
|
|
|
1593 Strategy:
|
|
|
1594 L-INS-i (Probably most accurate, very slow)
|
|
|
1595 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1596
|
|
|
1597 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1598 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1599
|
|
|
1600 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1601 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1602 To disable this change, add the --leavegappyregion option.
|
|
|
1603
|
|
|
1604 inputfile = orig
|
|
|
1605 2 x 70 - 70 d
|
|
|
1606 outputhat23=1
|
|
|
1607 treein = 0
|
|
|
1608 compacttree = 0
|
|
|
1609 stacksize: 8192 kb
|
|
|
1610 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1611 All-to-all alignment.
|
|
|
1612 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1613 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1614 1 thread(s)
|
|
|
1615
|
|
|
1616 outputhat23=1
|
|
|
1617 Loading 'hat3.seed' ...
|
|
|
1618 done.
|
|
|
1619 Writing hat3 for iterative refinement
|
|
|
1620 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1621 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1622 tbutree = 1, compacttree = 0
|
|
|
1623 Constructing a UPGMA tree ...
|
|
|
1624
0 / 2
|
|
|
1625 done.
|
|
|
1626
|
|
|
1627 Progressive alignment ...
|
|
|
1628
STEP 1 /1 (thread 0)
|
|
|
1629 done.
|
|
|
1630 tbfast (nuc) Version 7.407
|
|
|
1631 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1632 1 thread(s)
|
|
|
1633
|
|
|
1634 minimumweight = 0.000010
|
|
|
1635 autosubalignment = 0.000000
|
|
|
1636 nthread = 1
|
|
|
1637 randomseed = 0
|
|
|
1638 blosum 62 / kimura 200
|
|
|
1639 poffset = 0
|
|
|
1640 niter = 1
|
|
|
1641 sueff_global = 0.100000
|
|
|
1642 nadd = 1
|
|
|
1643 Loading 'hat3' ... done.
|
|
|
1644 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1645
|
|
|
1646
0 / 2
|
|
|
1647 Segment 1/ 1 1- 89
|
|
|
1648 001-0000-1 (thread 1) identical
|
|
|
1649 Converged.
|
|
|
1650
|
|
|
1651 Reached 1
|
|
|
1652 done
|
|
|
1653 dvtditr (nuc) Version 7.407
|
|
|
1654 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1655 1 thread(s)
|
|
|
1656
|
|
|
1657
|
|
|
1658 Strategy:
|
|
|
1659 L-INS-i (Probably most accurate, very slow)
|
|
|
1660 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1661
|
|
|
1662 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1663 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1664
|
|
|
1665 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1666 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1667 To disable this change, add the --leavegappyregion option.
|
|
|
1668
|
|
|
1669 inputfile = orig
|
|
|
1670 3 x 95 - 70 d
|
|
|
1671 nadd = 1
|
|
|
1672 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1673
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
1674 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1675 1 thread(s)
|
|
|
1676
|
|
|
1677 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1678 All-to-all alignment.
|
|
|
1679
|
|
|
1680
|
|
|
1681 ##### writing hat3
|
|
|
1682 pairlocalalign (nuc) Version 7.407
|
|
|
1683 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1684 1 thread(s)
|
|
|
1685
|
|
|
1686 nadd = 1
|
|
|
1687 ppenalty_ex = -10
|
|
|
1688 nthread = 1
|
|
|
1689 blosum 62 / kimura 200
|
|
|
1690 sueff_global = 0.100000
|
|
|
1691 norg = 2
|
|
|
1692 njobc = 3
|
|
|
1693 Loading 'hat3' ...
|
|
|
1694 done.
|
|
|
1695 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1696 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
1697 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
1698
0 / 1 (thread 0)
c
|
|
|
1699
|
|
|
1700 Combining ..
|
|
|
1701 0 / 1
0 / 1
done.
|
|
|
1702
|
|
|
1703
done.
|
|
|
1704
|
|
|
1705 addsingle (nuc) Version 7.407
|
|
|
1706 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1707 1 thread(s)
|
|
|
1708
|
|
|
1709
|
|
|
1710 Strategy:
|
|
|
1711 Multi-INS-fragment (Not tested.)
|
|
|
1712 ?
|
|
|
1713
|
|
|
1714 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1715 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1716
|
|
|
1717 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1718 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1719 To disable this change, add the --leavegappyregion option.
|
|
|
1720
|
|
|
1721 inputfile = orig
|
|
|
1722 2 x 70 - 70 d
|
|
|
1723 outputhat23=1
|
|
|
1724 treein = 0
|
|
|
1725 compacttree = 0
|
|
|
1726 stacksize: 8192 kb
|
|
|
1727 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1728 All-to-all alignment.
|
|
|
1729 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
|
|
|
1730 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1731 1 thread(s)
|
|
|
1732
|
|
|
1733 outputhat23=1
|
|
|
1734 Loading 'hat3.seed' ...
|
|
|
1735 done.
|
|
|
1736 Writing hat3 for iterative refinement
|
|
|
1737 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1738 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1739 tbutree = 1, compacttree = 0
|
|
|
1740 Constructing a UPGMA tree ...
|
|
|
1741
0 / 2
|
|
|
1742 done.
|
|
|
1743
|
|
|
1744 Progressive alignment ...
|
|
|
1745
STEP 1 /1 (thread 0)
|
|
|
1746 done.
|
|
|
1747 tbfast (nuc) Version 7.407
|
|
|
1748 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1749 1 thread(s)
|
|
|
1750
|
|
|
1751 minimumweight = 0.000010
|
|
|
1752 autosubalignment = 0.000000
|
|
|
1753 nthread = 1
|
|
|
1754 randomseed = 0
|
|
|
1755 blosum 62 / kimura 200
|
|
|
1756 poffset = 0
|
|
|
1757 niter = 1
|
|
|
1758 sueff_global = 0.100000
|
|
|
1759 nadd = 1
|
|
|
1760 Loading 'hat3' ... done.
|
|
|
1761 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1762
|
|
|
1763
0 / 2
|
|
|
1764 Segment 1/ 1 1- 95
|
|
|
1765 001-0000-1 (thread 1) identical
|
|
|
1766 Converged.
|
|
|
1767
|
|
|
1768 Reached 1
|
|
|
1769 done
|
|
|
1770 dvtditr (nuc) Version 7.407
|
|
|
1771 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1772 1 thread(s)
|
|
|
1773
|
|
|
1774
|
|
|
1775 Strategy:
|
|
|
1776 L-INS-i (Probably most accurate, very slow)
|
|
|
1777 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
1778
|
|
|
1779 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1780 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1781
|
|
|
1782 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1783 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1784 To disable this change, add the --leavegappyregion option.
|
|
|
1785
|
|
|
1786 inputfile = orig
|
|
|
1787 3 x 71 - 70 d
|
|
|
1788 nadd = 1
|
|
|
1789 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1790
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
1791 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1792 1 thread(s)
|
|
|
1793
|
|
|
1794 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1795 All-to-all alignment.
|
|
|
1796
|
|
|
1797
|
|
|
1798 ##### writing hat3
|
|
|
1799 pairlocalalign (nuc) Version 7.407
|
|
|
1800 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1801 1 thread(s)
|
|
|
1802
|
|
|
1803 nadd = 1
|
|
|
1804 ppenalty_ex = -10
|
|
|
1805 nthread = 1
|
|
|
1806 blosum 62 / kimura 200
|
|
|
1807 sueff_global = 0.100000
|
|
|
1808 norg = 2
|
|
|
1809 njobc = 3
|
|
|
1810 Loading 'hat3' ...
|
|
|
1811 done.
|
|
|
1812 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1813 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
1814 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
1815
0 / 1 (thread 0)
c
|
|
|
1816
|
|
|
1817 Combining ..
|
|
|
1818 0 / 1
0 / 1
done.
|
|
|
1819
|
|
|
1820
done.
|
|
|
1821
|
|
|
1822 addsingle (nuc) Version 7.407
|
|
|
1823 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1824 1 thread(s)
|
|
|
1825
|
|
|
1826
|
|
|
1827 Strategy:
|
|
|
1828 Multi-INS-fragment (Not tested.)
|
|
|
1829 ?
|
|
|
1830
|
|
|
1831 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1832 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1833
|
|
|
1834 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1835 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1836 To disable this change, add the --leavegappyregion option.
|
|
|
1837
|
|
|
1838 inputfile = orig
|
|
|
1839 5 x 110 - 70 d
|
|
|
1840 nadd = 1
|
|
|
1841 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1842
0 / 4 (thread 0)dndpre (nuc) Version 7.407
|
|
|
1843 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1844 1 thread(s)
|
|
|
1845
|
|
|
1846 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1847 All-to-all alignment.
|
|
|
1848
|
|
|
1849
|
|
|
1850 ##### writing hat3
|
|
|
1851 pairlocalalign (nuc) Version 7.407
|
|
|
1852 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1853 1 thread(s)
|
|
|
1854
|
|
|
1855 nadd = 1
|
|
|
1856 ppenalty_ex = -10
|
|
|
1857 nthread = 1
|
|
|
1858 blosum 62 / kimura 200
|
|
|
1859 sueff_global = 0.100000
|
|
|
1860 norg = 4
|
|
|
1861 njobc = 5
|
|
|
1862 Loading 'hat3' ...
|
|
|
1863 done.
|
|
|
1864 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1865 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
1866 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
1867
0 / 1 (thread 0)
c
|
|
|
1868
|
|
|
1869 Combining ..
|
|
|
1870 0 / 1
0 / 1
done.
|
|
|
1871
|
|
|
1872
done.
|
|
|
1873
|
|
|
1874 addsingle (nuc) Version 7.407
|
|
|
1875 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1876 1 thread(s)
|
|
|
1877
|
|
|
1878
|
|
|
1879 Strategy:
|
|
|
1880 Multi-INS-fragment (Not tested.)
|
|
|
1881 ?
|
|
|
1882
|
|
|
1883 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1884 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1885
|
|
|
1886 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1887 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1888 To disable this change, add the --leavegappyregion option.
|
|
|
1889
|
|
|
1890 inputfile = orig
|
|
|
1891 3 x 90 - 70 d
|
|
|
1892 nadd = 1
|
|
|
1893 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1894
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
1895 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1896 1 thread(s)
|
|
|
1897
|
|
|
1898 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1899 All-to-all alignment.
|
|
|
1900
|
|
|
1901
|
|
|
1902 ##### writing hat3
|
|
|
1903 pairlocalalign (nuc) Version 7.407
|
|
|
1904 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
1905 1 thread(s)
|
|
|
1906
|
|
|
1907 nadd = 1
|
|
|
1908 ppenalty_ex = -10
|
|
|
1909 nthread = 1
|
|
|
1910 blosum 62 / kimura 200
|
|
|
1911 sueff_global = 0.100000
|
|
|
1912 norg = 2
|
|
|
1913 njobc = 3
|
|
|
1914 Loading 'hat3' ...
|
|
|
1915 done.
|
|
|
1916 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1917 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
1918 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
1919
0 / 1 (thread 0)
c
|
|
|
1920
|
|
|
1921 Combining ..
|
|
|
1922 0 / 1
0 / 1
done.
|
|
|
1923
|
|
|
1924
done.
|
|
|
1925
|
|
|
1926 addsingle (nuc) Version 7.407
|
|
|
1927 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1928 1 thread(s)
|
|
|
1929
|
|
|
1930
|
|
|
1931 Strategy:
|
|
|
1932 Multi-INS-fragment (Not tested.)
|
|
|
1933 ?
|
|
|
1934
|
|
|
1935 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
1936 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
1937
|
|
|
1938 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
1939 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
1940 To disable this change, add the --leavegappyregion option.
|
|
|
1941
|
|
|
1942 inputfile = orig
|
|
|
1943 4 x 107 - 99 d
|
|
|
1944 nthread = 1
|
|
|
1945 nthreadpair = 1
|
|
|
1946 nthreadtb = 1
|
|
|
1947 ppenalty_ex = 0
|
|
|
1948 stacksize: 8192 kb
|
|
|
1949 nsubalignments = 2
|
|
|
1950 maxmem = 2
|
|
|
1951 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
1952 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
1953
|
|
|
1954
|
|
|
1955
|
|
|
1956 Making a distance matrix ..
|
|
|
1957
1 / 4 (thread 0)
|
|
|
1958 done.
|
|
|
1959
|
|
|
1960 Constructing a UPGMA tree ...
|
|
|
1961
|
|
|
1962
0 / 4
|
|
|
1963 ###################################################################
|
|
|
1964 # WARNING: Group 2 is forced to be a monophyletic cluster.
|
|
|
1965 ###################################################################
|
|
|
1966 Reallocated inconsistentpairlist, size=2
|
|
|
1967
|
|
|
1968 done.
|
|
|
1969
|
|
|
1970 Checking subalignment 1:
|
|
|
1971 -> OK
|
|
|
1972 Checking subalignment 2:
|
|
|
1973 -> OK
|
|
|
1974 Progressive alignment 1/2...
|
|
|
1975
STEP 3 / 3 (thread 0) f
|
|
|
1976 done.
|
|
|
1977
|
|
|
1978 Making a distance matrix from msa..
|
|
|
1979
0 / 4 (thread 0)
|
|
|
1980 done.
|
|
|
1981
|
|
|
1982 Constructing a UPGMA tree ...
|
|
|
1983
|
|
|
1984
0 / 4
|
|
|
1985 done.
|
|
|
1986
|
|
|
1987 Checking subalignment 1:
|
|
|
1988 -> OK
|
|
|
1989 Checking subalignment 2:
|
|
|
1990 -> OK
|
|
|
1991 Progressive alignment 2/2...
|
|
|
1992
STEP 3 / 3 (thread 0) f
|
|
|
1993 done.
|
|
|
1994
|
|
|
1995 disttbfast (nuc) Version 7.407
|
|
|
1996 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
1997 1 thread(s)
|
|
|
1998
|
|
|
1999 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2000
0 / 4 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2001 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
2002 1 thread(s)
|
|
|
2003
|
|
|
2004 minimumweight = 0.000010
|
|
|
2005 autosubalignment = 0.000000
|
|
|
2006 nthread = 1
|
|
|
2007 randomseed = 0
|
|
|
2008 blosum 62 / kimura 200
|
|
|
2009 poffset = 0
|
|
|
2010 niter = 1
|
|
|
2011 sueff_global = 0.100000
|
|
|
2012 nadd = 1
|
|
|
2013 nsubalignments = 2
|
|
|
2014 maxmem = 2
|
|
|
2015 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2016
|
|
|
2017
|
|
|
2018
0 / 4
|
|
|
2019
|
|
|
2020 Checking subalignment 1:
|
|
|
2021 1 2
|
|
|
2022 -> OK
|
|
|
2023
|
|
|
2024 Checking subalignment 2:
|
|
|
2025 3 4
|
|
|
2026 -> OK
|
|
|
2027 Segment 1/ 1 1- 156
|
|
|
2028 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-1 (thread 1) identical
001-0004-1 (thread 1) worse
|
|
|
2029 Converged.
|
|
|
2030
|
|
|
2031 Reached 1
|
|
|
2032 done
|
|
|
2033 dvtditr (nuc) Version 7.407
|
|
|
2034 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2035 1 thread(s)
|
|
|
2036
|
|
|
2037
|
|
|
2038 Strategy:
|
|
|
2039 FFT-NS-i (Standard)
|
|
|
2040 Iterative refinement method (max. 1 iterations)
|
|
|
2041
|
|
|
2042 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2043 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2044
|
|
|
2045 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2046 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2047 To disable this change, add the --leavegappyregion option.
|
|
|
2048
|
|
|
2049 inputfile = orig
|
|
|
2050 5 x 91 - 78 d
|
|
|
2051 nthread = 1
|
|
|
2052 nthreadpair = 1
|
|
|
2053 nthreadtb = 1
|
|
|
2054 ppenalty_ex = 0
|
|
|
2055 stacksize: 8192 kb
|
|
|
2056 nsubalignments = 2
|
|
|
2057 maxmem = 3
|
|
|
2058 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2059 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
2060
|
|
|
2061
|
|
|
2062
|
|
|
2063 Making a distance matrix ..
|
|
|
2064
1 / 5 (thread 0)
|
|
|
2065 done.
|
|
|
2066
|
|
|
2067 Constructing a UPGMA tree ...
|
|
|
2068
|
|
|
2069
0 / 5
|
|
|
2070 done.
|
|
|
2071
|
|
|
2072 Checking subalignment 1:
|
|
|
2073 -> OK
|
|
|
2074 Checking subalignment 2:
|
|
|
2075 -> OK
|
|
|
2076 Progressive alignment 1/2...
|
|
|
2077
STEP 4 / 4 (thread 0) f
|
|
|
2078 done.
|
|
|
2079
|
|
|
2080 Making a distance matrix from msa..
|
|
|
2081
0 / 5 (thread 0)
|
|
|
2082 done.
|
|
|
2083
|
|
|
2084 Constructing a UPGMA tree ...
|
|
|
2085
|
|
|
2086
0 / 5
|
|
|
2087 done.
|
|
|
2088
|
|
|
2089 Checking subalignment 1:
|
|
|
2090 -> OK
|
|
|
2091 Checking subalignment 2:
|
|
|
2092 -> OK
|
|
|
2093 Progressive alignment 2/2...
|
|
|
2094
STEP 4 / 4 (thread 0) f
|
|
|
2095 done.
|
|
|
2096
|
|
|
2097 disttbfast (nuc) Version 7.407
|
|
|
2098 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2099 1 thread(s)
|
|
|
2100
|
|
|
2101 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2102
0 / 5 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2103 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
2104 1 thread(s)
|
|
|
2105
|
|
|
2106 minimumweight = 0.000010
|
|
|
2107 autosubalignment = 0.000000
|
|
|
2108 nthread = 1
|
|
|
2109 randomseed = 0
|
|
|
2110 blosum 62 / kimura 200
|
|
|
2111 poffset = 0
|
|
|
2112 niter = 1
|
|
|
2113 sueff_global = 0.100000
|
|
|
2114 nadd = 1
|
|
|
2115 nsubalignments = 2
|
|
|
2116 maxmem = 3
|
|
|
2117 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2118
|
|
|
2119
|
|
|
2120
0 / 5
|
|
|
2121
|
|
|
2122 Checking subalignment 1:
|
|
|
2123 1 2
|
|
|
2124 -> OK
|
|
|
2125
|
|
|
2126 Checking subalignment 2:
|
|
|
2127 3 4 5
|
|
|
2128 -> OK
|
|
|
2129 Segment 1/ 1 1- 108
|
|
|
2130 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-1 (thread 1) identical
001-0006-1 (thread 1) better
|
|
|
2131 Reached 1
|
|
|
2132 done
|
|
|
2133 dvtditr (nuc) Version 7.407
|
|
|
2134 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2135 1 thread(s)
|
|
|
2136
|
|
|
2137
|
|
|
2138 Strategy:
|
|
|
2139 FFT-NS-i (Standard)
|
|
|
2140 Iterative refinement method (max. 1 iterations)
|
|
|
2141
|
|
|
2142 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2143 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2144
|
|
|
2145 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2146 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2147 To disable this change, add the --leavegappyregion option.
|
|
|
2148
|
|
|
2149 inputfile = orig
|
|
|
2150 4 x 117 - 114 d
|
|
|
2151 nthread = 1
|
|
|
2152 nthreadpair = 1
|
|
|
2153 nthreadtb = 1
|
|
|
2154 ppenalty_ex = 0
|
|
|
2155 stacksize: 8192 kb
|
|
|
2156 nsubalignments = 2
|
|
|
2157 maxmem = 2
|
|
|
2158 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2159 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
2160
|
|
|
2161
|
|
|
2162
|
|
|
2163 Making a distance matrix ..
|
|
|
2164
1 / 4 (thread 0)
|
|
|
2165 done.
|
|
|
2166
|
|
|
2167 Constructing a UPGMA tree ...
|
|
|
2168
|
|
|
2169
0 / 4
|
|
|
2170 done.
|
|
|
2171
|
|
|
2172 Checking subalignment 1:
|
|
|
2173 -> OK
|
|
|
2174 Checking subalignment 2:
|
|
|
2175 -> OK
|
|
|
2176 Progressive alignment 1/2...
|
|
|
2177
STEP 3 / 3 (thread 0) f
|
|
|
2178 done.
|
|
|
2179
|
|
|
2180 Making a distance matrix from msa..
|
|
|
2181
0 / 4 (thread 0)
|
|
|
2182 done.
|
|
|
2183
|
|
|
2184 Constructing a UPGMA tree ...
|
|
|
2185
|
|
|
2186
0 / 4
|
|
|
2187 done.
|
|
|
2188
|
|
|
2189 Checking subalignment 1:
|
|
|
2190 -> OK
|
|
|
2191 Checking subalignment 2:
|
|
|
2192 -> OK
|
|
|
2193 Progressive alignment 2/2...
|
|
|
2194
STEP 3 / 3 (thread 0) f
|
|
|
2195 done.
|
|
|
2196
|
|
|
2197 disttbfast (nuc) Version 7.407
|
|
|
2198 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2199 1 thread(s)
|
|
|
2200
|
|
|
2201 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2202
0 / 4 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2203 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
2204 1 thread(s)
|
|
|
2205
|
|
|
2206 minimumweight = 0.000010
|
|
|
2207 autosubalignment = 0.000000
|
|
|
2208 nthread = 1
|
|
|
2209 randomseed = 0
|
|
|
2210 blosum 62 / kimura 200
|
|
|
2211 poffset = 0
|
|
|
2212 niter = 1
|
|
|
2213 sueff_global = 0.100000
|
|
|
2214 nadd = 1
|
|
|
2215 nsubalignments = 2
|
|
|
2216 maxmem = 2
|
|
|
2217 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2218
|
|
|
2219
|
|
|
2220
0 / 4
|
|
|
2221
|
|
|
2222 Checking subalignment 1:
|
|
|
2223 1 2
|
|
|
2224 -> OK
|
|
|
2225
|
|
|
2226 Checking subalignment 2:
|
|
|
2227 3 4
|
|
|
2228 -> OK
|
|
|
2229 Segment 1/ 2 1- 62
|
|
|
2230 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-1 (thread 1) identical
|
|
|
2231 Converged.
|
|
|
2232
|
|
|
2233 Reached 1
|
|
|
2234 Segment 2/ 2 62- 134
|
|
|
2235 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-1 (thread 1) identical
001-0004-1 (thread 1) better
|
|
|
2236 Reached 1
|
|
|
2237 done
|
|
|
2238 dvtditr (nuc) Version 7.407
|
|
|
2239 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2240 1 thread(s)
|
|
|
2241
|
|
|
2242
|
|
|
2243 Strategy:
|
|
|
2244 FFT-NS-i (Standard)
|
|
|
2245 Iterative refinement method (max. 1 iterations)
|
|
|
2246
|
|
|
2247 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2248 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2249
|
|
|
2250 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2251 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2252 To disable this change, add the --leavegappyregion option.
|
|
|
2253
|
|
|
2254 inputfile = orig
|
|
|
2255 3 x 78 - 70 d
|
|
|
2256 nadd = 1
|
|
|
2257 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2258
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2259 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2260 1 thread(s)
|
|
|
2261
|
|
|
2262 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2263 All-to-all alignment.
|
|
|
2264
|
|
|
2265
|
|
|
2266 ##### writing hat3
|
|
|
2267 pairlocalalign (nuc) Version 7.407
|
|
|
2268 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2269 1 thread(s)
|
|
|
2270
|
|
|
2271 nadd = 1
|
|
|
2272 ppenalty_ex = -10
|
|
|
2273 nthread = 1
|
|
|
2274 blosum 62 / kimura 200
|
|
|
2275 sueff_global = 0.100000
|
|
|
2276 norg = 2
|
|
|
2277 njobc = 3
|
|
|
2278 Loading 'hat3' ...
|
|
|
2279 done.
|
|
|
2280 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2281 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
2282 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
2283
0 / 1 (thread 0)
c
|
|
|
2284
|
|
|
2285 Combining ..
|
|
|
2286 0 / 1
0 / 1
done.
|
|
|
2287
|
|
|
2288
done.
|
|
|
2289
|
|
|
2290 addsingle (nuc) Version 7.407
|
|
|
2291 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2292 1 thread(s)
|
|
|
2293
|
|
|
2294
|
|
|
2295 Strategy:
|
|
|
2296 Multi-INS-fragment (Not tested.)
|
|
|
2297 ?
|
|
|
2298
|
|
|
2299 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2300 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2301
|
|
|
2302 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2303 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2304 To disable this change, add the --leavegappyregion option.
|
|
|
2305
|
|
|
2306 inputfile = orig
|
|
|
2307 4 x 102 - 70 d
|
|
|
2308 nadd = 1
|
|
|
2309 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2310
0 / 3 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2311 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2312 1 thread(s)
|
|
|
2313
|
|
|
2314 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2315 All-to-all alignment.
|
|
|
2316
|
|
|
2317
|
|
|
2318 ##### writing hat3
|
|
|
2319 pairlocalalign (nuc) Version 7.407
|
|
|
2320 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2321 1 thread(s)
|
|
|
2322
|
|
|
2323 nadd = 1
|
|
|
2324 ppenalty_ex = -10
|
|
|
2325 nthread = 1
|
|
|
2326 blosum 62 / kimura 200
|
|
|
2327 sueff_global = 0.100000
|
|
|
2328 norg = 3
|
|
|
2329 njobc = 4
|
|
|
2330 Loading 'hat3' ...
|
|
|
2331 done.
|
|
|
2332 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2333 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
2334 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
2335
0 / 1 (thread 0)
c
|
|
|
2336
|
|
|
2337 Combining ..
|
|
|
2338 0 / 1
0 / 1
done.
|
|
|
2339
|
|
|
2340
done.
|
|
|
2341
|
|
|
2342 addsingle (nuc) Version 7.407
|
|
|
2343 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2344 1 thread(s)
|
|
|
2345
|
|
|
2346
|
|
|
2347 Strategy:
|
|
|
2348 Multi-INS-fragment (Not tested.)
|
|
|
2349 ?
|
|
|
2350
|
|
|
2351 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2352 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2353
|
|
|
2354 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2355 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2356 To disable this change, add the --leavegappyregion option.
|
|
|
2357
|
|
|
2358 inputfile = orig
|
|
|
2359 5 x 84 - 70 d
|
|
|
2360 nadd = 1
|
|
|
2361 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2362
0 / 4 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2363 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2364 1 thread(s)
|
|
|
2365
|
|
|
2366 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2367 All-to-all alignment.
|
|
|
2368
|
|
|
2369
|
|
|
2370 ##### writing hat3
|
|
|
2371 pairlocalalign (nuc) Version 7.407
|
|
|
2372 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2373 1 thread(s)
|
|
|
2374
|
|
|
2375 nadd = 1
|
|
|
2376 ppenalty_ex = -10
|
|
|
2377 nthread = 1
|
|
|
2378 blosum 62 / kimura 200
|
|
|
2379 sueff_global = 0.100000
|
|
|
2380 norg = 4
|
|
|
2381 njobc = 5
|
|
|
2382 Loading 'hat3' ...
|
|
|
2383 done.
|
|
|
2384 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2385 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
2386 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
2387
0 / 1 (thread 0)
c
|
|
|
2388
|
|
|
2389 Combining ..
|
|
|
2390 0 / 1
0 / 1
done.
|
|
|
2391
|
|
|
2392
done.
|
|
|
2393
|
|
|
2394 addsingle (nuc) Version 7.407
|
|
|
2395 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2396 1 thread(s)
|
|
|
2397
|
|
|
2398
|
|
|
2399 Strategy:
|
|
|
2400 Multi-INS-fragment (Not tested.)
|
|
|
2401 ?
|
|
|
2402
|
|
|
2403 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2404 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2405
|
|
|
2406 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2407 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2408 To disable this change, add the --leavegappyregion option.
|
|
|
2409
|
|
|
2410 inputfile = orig
|
|
|
2411 3 x 72 - 70 d
|
|
|
2412 nadd = 1
|
|
|
2413 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2414
0 / 2 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2415 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2416 1 thread(s)
|
|
|
2417
|
|
|
2418 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2419 All-to-all alignment.
|
|
|
2420
|
|
|
2421
|
|
|
2422 ##### writing hat3
|
|
|
2423 pairlocalalign (nuc) Version 7.407
|
|
|
2424 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2425 1 thread(s)
|
|
|
2426
|
|
|
2427 nadd = 1
|
|
|
2428 ppenalty_ex = -10
|
|
|
2429 nthread = 1
|
|
|
2430 blosum 62 / kimura 200
|
|
|
2431 sueff_global = 0.100000
|
|
|
2432 norg = 2
|
|
|
2433 njobc = 3
|
|
|
2434 Loading 'hat3' ...
|
|
|
2435 done.
|
|
|
2436 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2437 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
2438 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
2439
0 / 1 (thread 0)
c
|
|
|
2440
|
|
|
2441 Combining ..
|
|
|
2442 0 / 1
0 / 1
done.
|
|
|
2443
|
|
|
2444
done.
|
|
|
2445
|
|
|
2446 addsingle (nuc) Version 7.407
|
|
|
2447 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2448 1 thread(s)
|
|
|
2449
|
|
|
2450
|
|
|
2451 Strategy:
|
|
|
2452 Multi-INS-fragment (Not tested.)
|
|
|
2453 ?
|
|
|
2454
|
|
|
2455 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2456 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2457
|
|
|
2458 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2459 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2460 To disable this change, add the --leavegappyregion option.
|
|
|
2461
|
|
|
2462 inputfile = orig
|
|
|
2463 4 x 99 - 76 d
|
|
|
2464 nthread = 1
|
|
|
2465 nthreadpair = 1
|
|
|
2466 nthreadtb = 1
|
|
|
2467 ppenalty_ex = 0
|
|
|
2468 stacksize: 8192 kb
|
|
|
2469 nsubalignments = 2
|
|
|
2470 maxmem = 2
|
|
|
2471 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2472 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
2473
|
|
|
2474
|
|
|
2475
|
|
|
2476 Making a distance matrix ..
|
|
|
2477
1 / 4 (thread 0)
|
|
|
2478 done.
|
|
|
2479
|
|
|
2480 Constructing a UPGMA tree ...
|
|
|
2481
|
|
|
2482
0 / 4
|
|
|
2483 ###################################################################
|
|
|
2484 # WARNING: Group 2 is forced to be a monophyletic cluster.
|
|
|
2485 ###################################################################
|
|
|
2486
|
|
|
2487 done.
|
|
|
2488
|
|
|
2489 Checking subalignment 1:
|
|
|
2490 -> OK
|
|
|
2491 Checking subalignment 2:
|
|
|
2492 -> OK
|
|
|
2493 Progressive alignment 1/2...
|
|
|
2494
STEP 3 / 3 (thread 0) f
|
|
|
2495 done.
|
|
|
2496
|
|
|
2497 Making a distance matrix from msa..
|
|
|
2498
0 / 4 (thread 0)
|
|
|
2499 done.
|
|
|
2500
|
|
|
2501 Constructing a UPGMA tree ...
|
|
|
2502
|
|
|
2503
0 / 4
|
|
|
2504 done.
|
|
|
2505
|
|
|
2506 Checking subalignment 1:
|
|
|
2507 -> OK
|
|
|
2508 Checking subalignment 2:
|
|
|
2509 -> OK
|
|
|
2510 Progressive alignment 2/2...
|
|
|
2511
STEP 3 / 3 (thread 0) f
|
|
|
2512 done.
|
|
|
2513
|
|
|
2514 disttbfast (nuc) Version 7.407
|
|
|
2515 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2516 1 thread(s)
|
|
|
2517
|
|
|
2518 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2519
0 / 4 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2520 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
2521 1 thread(s)
|
|
|
2522
|
|
|
2523 minimumweight = 0.000010
|
|
|
2524 autosubalignment = 0.000000
|
|
|
2525 nthread = 1
|
|
|
2526 randomseed = 0
|
|
|
2527 blosum 62 / kimura 200
|
|
|
2528 poffset = 0
|
|
|
2529 niter = 1
|
|
|
2530 sueff_global = 0.100000
|
|
|
2531 nadd = 1
|
|
|
2532 nsubalignments = 2
|
|
|
2533 maxmem = 2
|
|
|
2534 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2535
|
|
|
2536
|
|
|
2537
0 / 4
|
|
|
2538
|
|
|
2539 Checking subalignment 1:
|
|
|
2540 1 2
|
|
|
2541 -> OK
|
|
|
2542
|
|
|
2543 Checking subalignment 2:
|
|
|
2544 3 4
|
|
|
2545 -> OK
|
|
|
2546 Segment 1/ 1 1- 103
|
|
|
2547 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-1 (thread 1) identical
001-0004-1 (thread 1) better
|
|
|
2548 Reached 1
|
|
|
2549 done
|
|
|
2550 dvtditr (nuc) Version 7.407
|
|
|
2551 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2552 1 thread(s)
|
|
|
2553
|
|
|
2554
|
|
|
2555 Strategy:
|
|
|
2556 FFT-NS-i (Standard)
|
|
|
2557 Iterative refinement method (max. 1 iterations)
|
|
|
2558
|
|
|
2559 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2560 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2561
|
|
|
2562 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2563 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2564 To disable this change, add the --leavegappyregion option.
|
|
|
2565
|
|
|
2566 inputfile = orig
|
|
|
2567 5 x 101 - 72 d
|
|
|
2568 nthread = 1
|
|
|
2569 nthreadpair = 1
|
|
|
2570 nthreadtb = 1
|
|
|
2571 ppenalty_ex = 0
|
|
|
2572 stacksize: 8192 kb
|
|
|
2573 nsubalignments = 2
|
|
|
2574 maxmem = 3
|
|
|
2575 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2576 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
2577
|
|
|
2578
|
|
|
2579
|
|
|
2580 Making a distance matrix ..
|
|
|
2581
1 / 5 (thread 0)
|
|
|
2582 done.
|
|
|
2583
|
|
|
2584 Constructing a UPGMA tree ...
|
|
|
2585
|
|
|
2586
0 / 5
|
|
|
2587 done.
|
|
|
2588
|
|
|
2589 Checking subalignment 1:
|
|
|
2590 -> OK
|
|
|
2591 Checking subalignment 2:
|
|
|
2592 -> OK
|
|
|
2593 Progressive alignment 1/2...
|
|
|
2594
STEP 4 / 4 (thread 0) f
|
|
|
2595 done.
|
|
|
2596
|
|
|
2597 Making a distance matrix from msa..
|
|
|
2598
0 / 5 (thread 0)
|
|
|
2599 done.
|
|
|
2600
|
|
|
2601 Constructing a UPGMA tree ...
|
|
|
2602
|
|
|
2603
0 / 5
|
|
|
2604 done.
|
|
|
2605
|
|
|
2606 Checking subalignment 1:
|
|
|
2607 -> OK
|
|
|
2608 Checking subalignment 2:
|
|
|
2609 -> OK
|
|
|
2610 Progressive alignment 2/2...
|
|
|
2611
STEP 4 / 4 (thread 0) f
|
|
|
2612 done.
|
|
|
2613
|
|
|
2614 disttbfast (nuc) Version 7.407
|
|
|
2615 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2616 1 thread(s)
|
|
|
2617
|
|
|
2618 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2619
0 / 5 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2620 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
2621 1 thread(s)
|
|
|
2622
|
|
|
2623 minimumweight = 0.000010
|
|
|
2624 autosubalignment = 0.000000
|
|
|
2625 nthread = 1
|
|
|
2626 randomseed = 0
|
|
|
2627 blosum 62 / kimura 200
|
|
|
2628 poffset = 0
|
|
|
2629 niter = 1
|
|
|
2630 sueff_global = 0.100000
|
|
|
2631 nadd = 1
|
|
|
2632 nsubalignments = 2
|
|
|
2633 maxmem = 3
|
|
|
2634 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2635
|
|
|
2636
|
|
|
2637
0 / 5
|
|
|
2638
|
|
|
2639 Checking subalignment 1:
|
|
|
2640 1 2 3
|
|
|
2641 -> OK
|
|
|
2642
|
|
|
2643 Checking subalignment 2:
|
|
|
2644 4 5
|
|
|
2645 -> OK
|
|
|
2646 Segment 1/ 1 1- 102
|
|
|
2647 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-1 (thread 1) identical
|
|
|
2648 Converged.
|
|
|
2649
|
|
|
2650 Reached 1
|
|
|
2651 done
|
|
|
2652 dvtditr (nuc) Version 7.407
|
|
|
2653 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2654 1 thread(s)
|
|
|
2655
|
|
|
2656
|
|
|
2657 Strategy:
|
|
|
2658 FFT-NS-i (Standard)
|
|
|
2659 Iterative refinement method (max. 1 iterations)
|
|
|
2660
|
|
|
2661 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2662 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2663
|
|
|
2664 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2665 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2666 To disable this change, add the --leavegappyregion option.
|
|
|
2667
|
|
|
2668 inputfile = orig
|
|
|
2669 4 x 95 - 71 d
|
|
|
2670 nthread = 1
|
|
|
2671 nthreadpair = 1
|
|
|
2672 nthreadtb = 1
|
|
|
2673 ppenalty_ex = 0
|
|
|
2674 stacksize: 8192 kb
|
|
|
2675 nsubalignments = 2
|
|
|
2676 maxmem = 2
|
|
|
2677 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2678 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
2679
|
|
|
2680
|
|
|
2681
|
|
|
2682 Making a distance matrix ..
|
|
|
2683
1 / 4 (thread 0)
|
|
|
2684 done.
|
|
|
2685
|
|
|
2686 Constructing a UPGMA tree ...
|
|
|
2687
|
|
|
2688
0 / 4
|
|
|
2689 done.
|
|
|
2690
|
|
|
2691 Checking subalignment 1:
|
|
|
2692 -> OK
|
|
|
2693 Checking subalignment 2:
|
|
|
2694 -> OK
|
|
|
2695 Progressive alignment 1/2...
|
|
|
2696
STEP 3 / 3 (thread 0) f
|
|
|
2697 done.
|
|
|
2698
|
|
|
2699 Making a distance matrix from msa..
|
|
|
2700
0 / 4 (thread 0)
|
|
|
2701 done.
|
|
|
2702
|
|
|
2703 Constructing a UPGMA tree ...
|
|
|
2704
|
|
|
2705
0 / 4
|
|
|
2706 done.
|
|
|
2707
|
|
|
2708 Checking subalignment 1:
|
|
|
2709 -> OK
|
|
|
2710 Checking subalignment 2:
|
|
|
2711 -> OK
|
|
|
2712 Progressive alignment 2/2...
|
|
|
2713
STEP 3 / 3 (thread 0) f
|
|
|
2714 done.
|
|
|
2715
|
|
|
2716 disttbfast (nuc) Version 7.407
|
|
|
2717 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2718 1 thread(s)
|
|
|
2719
|
|
|
2720 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2721
0 / 4 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2722 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
2723 1 thread(s)
|
|
|
2724
|
|
|
2725 minimumweight = 0.000010
|
|
|
2726 autosubalignment = 0.000000
|
|
|
2727 nthread = 1
|
|
|
2728 randomseed = 0
|
|
|
2729 blosum 62 / kimura 200
|
|
|
2730 poffset = 0
|
|
|
2731 niter = 1
|
|
|
2732 sueff_global = 0.100000
|
|
|
2733 nadd = 1
|
|
|
2734 nsubalignments = 2
|
|
|
2735 maxmem = 2
|
|
|
2736 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2737
|
|
|
2738
|
|
|
2739
0 / 4
|
|
|
2740
|
|
|
2741 Checking subalignment 1:
|
|
|
2742 1 2
|
|
|
2743 -> OK
|
|
|
2744
|
|
|
2745 Checking subalignment 2:
|
|
|
2746 3 4
|
|
|
2747 -> OK
|
|
|
2748 Segment 1/ 1 1- 114
|
|
|
2749 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-1 (thread 1) identical
001-0004-1 (thread 1) better
|
|
|
2750 Reached 1
|
|
|
2751 done
|
|
|
2752 dvtditr (nuc) Version 7.407
|
|
|
2753 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2754 1 thread(s)
|
|
|
2755
|
|
|
2756
|
|
|
2757 Strategy:
|
|
|
2758 FFT-NS-i (Standard)
|
|
|
2759 Iterative refinement method (max. 1 iterations)
|
|
|
2760
|
|
|
2761 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2762 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2763
|
|
|
2764 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2765 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2766 To disable this change, add the --leavegappyregion option.
|
|
|
2767
|
|
|
2768 inputfile = orig
|
|
|
2769 4 x 102 - 70 d
|
|
|
2770 nadd = 1
|
|
|
2771 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2772
0 / 3 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2773 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2774 1 thread(s)
|
|
|
2775
|
|
|
2776 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2777 All-to-all alignment.
|
|
|
2778
|
|
|
2779
|
|
|
2780 ##### writing hat3
|
|
|
2781 pairlocalalign (nuc) Version 7.407
|
|
|
2782 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2783 1 thread(s)
|
|
|
2784
|
|
|
2785 nadd = 1
|
|
|
2786 ppenalty_ex = -10
|
|
|
2787 nthread = 1
|
|
|
2788 blosum 62 / kimura 200
|
|
|
2789 sueff_global = 0.100000
|
|
|
2790 norg = 3
|
|
|
2791 njobc = 4
|
|
|
2792 Loading 'hat3' ...
|
|
|
2793 done.
|
|
|
2794 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2795 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
2796 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
2797
0 / 1 (thread 0)
c
|
|
|
2798
|
|
|
2799 Combining ..
|
|
|
2800 0 / 1
0 / 1
done.
|
|
|
2801
|
|
|
2802
done.
|
|
|
2803
|
|
|
2804 addsingle (nuc) Version 7.407
|
|
|
2805 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2806 1 thread(s)
|
|
|
2807
|
|
|
2808
|
|
|
2809 Strategy:
|
|
|
2810 Multi-INS-fragment (Not tested.)
|
|
|
2811 ?
|
|
|
2812
|
|
|
2813 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2814 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2815
|
|
|
2816 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2817 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2818 To disable this change, add the --leavegappyregion option.
|
|
|
2819
|
|
|
2820 inputfile = orig
|
|
|
2821 6 x 115 - 96 d
|
|
|
2822 nthread = 1
|
|
|
2823 nthreadpair = 1
|
|
|
2824 nthreadtb = 1
|
|
|
2825 ppenalty_ex = 0
|
|
|
2826 stacksize: 8192 kb
|
|
|
2827 nsubalignments = 2
|
|
|
2828 maxmem = 3
|
|
|
2829 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2830 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
2831
|
|
|
2832
|
|
|
2833
|
|
|
2834 Making a distance matrix ..
|
|
|
2835
1 / 6 (thread 0)
|
|
|
2836 done.
|
|
|
2837
|
|
|
2838 Constructing a UPGMA tree ...
|
|
|
2839
|
|
|
2840
0 / 6
|
|
|
2841 done.
|
|
|
2842
|
|
|
2843 Checking subalignment 1:
|
|
|
2844 -> OK
|
|
|
2845 Checking subalignment 2:
|
|
|
2846 -> OK
|
|
|
2847 Progressive alignment 1/2...
|
|
|
2848
STEP 5 / 5 (thread 0) f
|
|
|
2849 done.
|
|
|
2850
|
|
|
2851 Making a distance matrix from msa..
|
|
|
2852
0 / 6 (thread 0)
|
|
|
2853 done.
|
|
|
2854
|
|
|
2855 Constructing a UPGMA tree ...
|
|
|
2856
|
|
|
2857
0 / 6
|
|
|
2858 done.
|
|
|
2859
|
|
|
2860 Checking subalignment 1:
|
|
|
2861 -> OK
|
|
|
2862 Checking subalignment 2:
|
|
|
2863 -> OK
|
|
|
2864 Progressive alignment 2/2...
|
|
|
2865
STEP 5 / 5 (thread 0) f
|
|
|
2866 done.
|
|
|
2867
|
|
|
2868 disttbfast (nuc) Version 7.407
|
|
|
2869 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2870 1 thread(s)
|
|
|
2871
|
|
|
2872 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2873
0 / 6 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2874 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
2875 1 thread(s)
|
|
|
2876
|
|
|
2877 minimumweight = 0.000010
|
|
|
2878 autosubalignment = 0.000000
|
|
|
2879 nthread = 1
|
|
|
2880 randomseed = 0
|
|
|
2881 blosum 62 / kimura 200
|
|
|
2882 poffset = 0
|
|
|
2883 niter = 1
|
|
|
2884 sueff_global = 0.100000
|
|
|
2885 nadd = 1
|
|
|
2886 nsubalignments = 2
|
|
|
2887 maxmem = 3
|
|
|
2888 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2889
|
|
|
2890
|
|
|
2891
0 / 6
|
|
|
2892
|
|
|
2893 Checking subalignment 1:
|
|
|
2894 1 2 3
|
|
|
2895 -> OK
|
|
|
2896
|
|
|
2897 Checking subalignment 2:
|
|
|
2898 4 5 6
|
|
|
2899 -> OK
|
|
|
2900 Segment 1/ 1 1- 154
|
|
|
2901 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-1 (thread 1) identical
001-0008-1 (thread 1) better
|
|
|
2902 Reached 1
|
|
|
2903 done
|
|
|
2904 dvtditr (nuc) Version 7.407
|
|
|
2905 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2906 1 thread(s)
|
|
|
2907
|
|
|
2908
|
|
|
2909 Strategy:
|
|
|
2910 FFT-NS-i (Standard)
|
|
|
2911 Iterative refinement method (max. 1 iterations)
|
|
|
2912
|
|
|
2913 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2914 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2915
|
|
|
2916 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2917 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2918 To disable this change, add the --leavegappyregion option.
|
|
|
2919
|
|
|
2920 inputfile = orig
|
|
|
2921 6 x 110 - 70 d
|
|
|
2922 nadd = 1
|
|
|
2923 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2924
0 / 5 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2925 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2926 1 thread(s)
|
|
|
2927
|
|
|
2928 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2929 All-to-all alignment.
|
|
|
2930
|
|
|
2931
|
|
|
2932 ##### writing hat3
|
|
|
2933 pairlocalalign (nuc) Version 7.407
|
|
|
2934 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2935 1 thread(s)
|
|
|
2936
|
|
|
2937 nadd = 1
|
|
|
2938 ppenalty_ex = -10
|
|
|
2939 nthread = 1
|
|
|
2940 blosum 62 / kimura 200
|
|
|
2941 sueff_global = 0.100000
|
|
|
2942 norg = 5
|
|
|
2943 njobc = 6
|
|
|
2944 Loading 'hat3' ...
|
|
|
2945 done.
|
|
|
2946 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2947 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
2948 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
2949
0 / 1 (thread 0)
c
|
|
|
2950
|
|
|
2951 Combining ..
|
|
|
2952 0 / 1
0 / 1
done.
|
|
|
2953
|
|
|
2954
done.
|
|
|
2955
|
|
|
2956 addsingle (nuc) Version 7.407
|
|
|
2957 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
2958 1 thread(s)
|
|
|
2959
|
|
|
2960
|
|
|
2961 Strategy:
|
|
|
2962 Multi-INS-fragment (Not tested.)
|
|
|
2963 ?
|
|
|
2964
|
|
|
2965 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
2966 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
2967
|
|
|
2968 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
2969 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
2970 To disable this change, add the --leavegappyregion option.
|
|
|
2971
|
|
|
2972 inputfile = orig
|
|
|
2973 4 x 108 - 70 d
|
|
|
2974 nadd = 1
|
|
|
2975 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2976
0 / 3 (thread 0)dndpre (nuc) Version 7.407
|
|
|
2977 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2978 1 thread(s)
|
|
|
2979
|
|
|
2980 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2981 All-to-all alignment.
|
|
|
2982
|
|
|
2983
|
|
|
2984 ##### writing hat3
|
|
|
2985 pairlocalalign (nuc) Version 7.407
|
|
|
2986 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
2987 1 thread(s)
|
|
|
2988
|
|
|
2989 nadd = 1
|
|
|
2990 ppenalty_ex = -10
|
|
|
2991 nthread = 1
|
|
|
2992 blosum 62 / kimura 200
|
|
|
2993 sueff_global = 0.100000
|
|
|
2994 norg = 3
|
|
|
2995 njobc = 4
|
|
|
2996 Loading 'hat3' ...
|
|
|
2997 done.
|
|
|
2998 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
2999 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
3000 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
3001
0 / 1 (thread 0)
c
|
|
|
3002
|
|
|
3003 Combining ..
|
|
|
3004 0 / 1
0 / 1
done.
|
|
|
3005
|
|
|
3006
done.
|
|
|
3007
|
|
|
3008 addsingle (nuc) Version 7.407
|
|
|
3009 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3010 1 thread(s)
|
|
|
3011
|
|
|
3012
|
|
|
3013 Strategy:
|
|
|
3014 Multi-INS-fragment (Not tested.)
|
|
|
3015 ?
|
|
|
3016
|
|
|
3017 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3018 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3019
|
|
|
3020 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3021 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3022 To disable this change, add the --leavegappyregion option.
|
|
|
3023
|
|
|
3024 inputfile = orig
|
|
|
3025 5 x 93 - 87 d
|
|
|
3026 nthread = 1
|
|
|
3027 nthreadpair = 1
|
|
|
3028 nthreadtb = 1
|
|
|
3029 ppenalty_ex = 0
|
|
|
3030 stacksize: 8192 kb
|
|
|
3031 nsubalignments = 2
|
|
|
3032 maxmem = 3
|
|
|
3033 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3034 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3035
|
|
|
3036
|
|
|
3037
|
|
|
3038 Making a distance matrix ..
|
|
|
3039
1 / 5 (thread 0)
|
|
|
3040 done.
|
|
|
3041
|
|
|
3042 Constructing a UPGMA tree ...
|
|
|
3043
|
|
|
3044
0 / 5
|
|
|
3045 done.
|
|
|
3046
|
|
|
3047 Checking subalignment 1:
|
|
|
3048 -> OK
|
|
|
3049 Checking subalignment 2:
|
|
|
3050 -> OK
|
|
|
3051 Progressive alignment 1/2...
|
|
|
3052
STEP 4 / 4 (thread 0) f
|
|
|
3053 done.
|
|
|
3054
|
|
|
3055 Making a distance matrix from msa..
|
|
|
3056
0 / 5 (thread 0)
|
|
|
3057 done.
|
|
|
3058
|
|
|
3059 Constructing a UPGMA tree ...
|
|
|
3060
|
|
|
3061
0 / 5
|
|
|
3062 done.
|
|
|
3063
|
|
|
3064 Checking subalignment 1:
|
|
|
3065 -> OK
|
|
|
3066 Checking subalignment 2:
|
|
|
3067 -> OK
|
|
|
3068 Progressive alignment 2/2...
|
|
|
3069
STEP 4 / 4 (thread 0) f
|
|
|
3070 done.
|
|
|
3071
|
|
|
3072 disttbfast (nuc) Version 7.407
|
|
|
3073 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3074 1 thread(s)
|
|
|
3075
|
|
|
3076 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3077
0 / 5 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3078 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3079 1 thread(s)
|
|
|
3080
|
|
|
3081 minimumweight = 0.000010
|
|
|
3082 autosubalignment = 0.000000
|
|
|
3083 nthread = 1
|
|
|
3084 randomseed = 0
|
|
|
3085 blosum 62 / kimura 200
|
|
|
3086 poffset = 0
|
|
|
3087 niter = 1
|
|
|
3088 sueff_global = 0.100000
|
|
|
3089 nadd = 1
|
|
|
3090 nsubalignments = 2
|
|
|
3091 maxmem = 3
|
|
|
3092 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3093
|
|
|
3094
|
|
|
3095
0 / 5
|
|
|
3096
|
|
|
3097 Checking subalignment 1:
|
|
|
3098 1 2
|
|
|
3099 -> OK
|
|
|
3100
|
|
|
3101 Checking subalignment 2:
|
|
|
3102 3 4 5
|
|
|
3103 -> OK
|
|
|
3104 Segment 1/ 1 1- 102
|
|
|
3105 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-1 (thread 1) identical
001-0006-1 (thread 1) better
|
|
|
3106 Reached 1
|
|
|
3107 done
|
|
|
3108 dvtditr (nuc) Version 7.407
|
|
|
3109 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3110 1 thread(s)
|
|
|
3111
|
|
|
3112
|
|
|
3113 Strategy:
|
|
|
3114 FFT-NS-i (Standard)
|
|
|
3115 Iterative refinement method (max. 1 iterations)
|
|
|
3116
|
|
|
3117 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3118 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3119
|
|
|
3120 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3121 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3122 To disable this change, add the --leavegappyregion option.
|
|
|
3123
|
|
|
3124 inputfile = orig
|
|
|
3125 8 x 98 - 87 d
|
|
|
3126 nthread = 1
|
|
|
3127 nthreadpair = 1
|
|
|
3128 nthreadtb = 1
|
|
|
3129 ppenalty_ex = 0
|
|
|
3130 stacksize: 8192 kb
|
|
|
3131 nsubalignments = 2
|
|
|
3132 maxmem = 5
|
|
|
3133 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3134 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3135
|
|
|
3136
|
|
|
3137
|
|
|
3138 Making a distance matrix ..
|
|
|
3139
1 / 8 (thread 0)
|
|
|
3140 done.
|
|
|
3141
|
|
|
3142 Constructing a UPGMA tree ...
|
|
|
3143
|
|
|
3144
0 / 8
|
|
|
3145 done.
|
|
|
3146
|
|
|
3147 Checking subalignment 1:
|
|
|
3148 -> OK
|
|
|
3149 Checking subalignment 2:
|
|
|
3150 -> OK
|
|
|
3151 Progressive alignment 1/2...
|
|
|
3152
STEP 7 / 7 (thread 0) f
|
|
|
3153 done.
|
|
|
3154
|
|
|
3155 Making a distance matrix from msa..
|
|
|
3156
0 / 8 (thread 0)
|
|
|
3157 done.
|
|
|
3158
|
|
|
3159 Constructing a UPGMA tree ...
|
|
|
3160
|
|
|
3161
0 / 8
|
|
|
3162 done.
|
|
|
3163
|
|
|
3164 Checking subalignment 1:
|
|
|
3165 -> OK
|
|
|
3166 Checking subalignment 2:
|
|
|
3167 -> OK
|
|
|
3168 Progressive alignment 2/2...
|
|
|
3169
STEP 7 / 7 (thread 0) f
|
|
|
3170 done.
|
|
|
3171
|
|
|
3172 disttbfast (nuc) Version 7.407
|
|
|
3173 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3174 1 thread(s)
|
|
|
3175
|
|
|
3176 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3177
0 / 8 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3178 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3179 1 thread(s)
|
|
|
3180
|
|
|
3181 minimumweight = 0.000010
|
|
|
3182 autosubalignment = 0.000000
|
|
|
3183 nthread = 1
|
|
|
3184 randomseed = 0
|
|
|
3185 blosum 62 / kimura 200
|
|
|
3186 poffset = 0
|
|
|
3187 niter = 1
|
|
|
3188 sueff_global = 0.100000
|
|
|
3189 nadd = 1
|
|
|
3190 nsubalignments = 2
|
|
|
3191 maxmem = 5
|
|
|
3192 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3193
|
|
|
3194
|
|
|
3195
0 / 8
|
|
|
3196
|
|
|
3197 Checking subalignment 1:
|
|
|
3198 1 2 3
|
|
|
3199 -> OK
|
|
|
3200
|
|
|
3201 Checking subalignment 2:
|
|
|
3202 4 5 6 7 8
|
|
|
3203 -> OK
|
|
|
3204 Segment 1/ 1 1- 105
|
|
|
3205 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-1 (thread 1) identical
|
|
|
3206 Converged.
|
|
|
3207
|
|
|
3208 Reached 1
|
|
|
3209 done
|
|
|
3210 dvtditr (nuc) Version 7.407
|
|
|
3211 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3212 1 thread(s)
|
|
|
3213
|
|
|
3214
|
|
|
3215 Strategy:
|
|
|
3216 FFT-NS-i (Standard)
|
|
|
3217 Iterative refinement method (max. 1 iterations)
|
|
|
3218
|
|
|
3219 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3220 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3221
|
|
|
3222 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3223 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3224 To disable this change, add the --leavegappyregion option.
|
|
|
3225
|
|
|
3226 inputfile = orig
|
|
|
3227 5 x 97 - 74 d
|
|
|
3228 nthread = 1
|
|
|
3229 nthreadpair = 1
|
|
|
3230 nthreadtb = 1
|
|
|
3231 ppenalty_ex = 0
|
|
|
3232 stacksize: 8192 kb
|
|
|
3233 nsubalignments = 2
|
|
|
3234 maxmem = 3
|
|
|
3235 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3236 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3237
|
|
|
3238
|
|
|
3239
|
|
|
3240 Making a distance matrix ..
|
|
|
3241
1 / 5 (thread 0)
|
|
|
3242 done.
|
|
|
3243
|
|
|
3244 Constructing a UPGMA tree ...
|
|
|
3245
|
|
|
3246
0 / 5
|
|
|
3247 done.
|
|
|
3248
|
|
|
3249 Checking subalignment 1:
|
|
|
3250 -> OK
|
|
|
3251 Checking subalignment 2:
|
|
|
3252 -> OK
|
|
|
3253 Progressive alignment 1/2...
|
|
|
3254
STEP 4 / 4 (thread 0) f
|
|
|
3255 done.
|
|
|
3256
|
|
|
3257 Making a distance matrix from msa..
|
|
|
3258
0 / 5 (thread 0)
|
|
|
3259 done.
|
|
|
3260
|
|
|
3261 Constructing a UPGMA tree ...
|
|
|
3262
|
|
|
3263
0 / 5
|
|
|
3264 done.
|
|
|
3265
|
|
|
3266 Checking subalignment 1:
|
|
|
3267 -> OK
|
|
|
3268 Checking subalignment 2:
|
|
|
3269 -> OK
|
|
|
3270 Progressive alignment 2/2...
|
|
|
3271
STEP 4 / 4 (thread 0) f
|
|
|
3272 done.
|
|
|
3273
|
|
|
3274 disttbfast (nuc) Version 7.407
|
|
|
3275 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3276 1 thread(s)
|
|
|
3277
|
|
|
3278 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3279
0 / 5 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3280 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3281 1 thread(s)
|
|
|
3282
|
|
|
3283 minimumweight = 0.000010
|
|
|
3284 autosubalignment = 0.000000
|
|
|
3285 nthread = 1
|
|
|
3286 randomseed = 0
|
|
|
3287 blosum 62 / kimura 200
|
|
|
3288 poffset = 0
|
|
|
3289 niter = 1
|
|
|
3290 sueff_global = 0.100000
|
|
|
3291 nadd = 1
|
|
|
3292 nsubalignments = 2
|
|
|
3293 maxmem = 3
|
|
|
3294 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3295
|
|
|
3296
|
|
|
3297
0 / 5
|
|
|
3298
|
|
|
3299 Checking subalignment 1:
|
|
|
3300 1 2 3
|
|
|
3301 -> OK
|
|
|
3302
|
|
|
3303 Checking subalignment 2:
|
|
|
3304 4 5
|
|
|
3305 -> OK
|
|
|
3306 Segment 1/ 1 1- 109
|
|
|
3307 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-1 (thread 1) identical
001-0006-1 (thread 1) better
|
|
|
3308 Reached 1
|
|
|
3309 done
|
|
|
3310 dvtditr (nuc) Version 7.407
|
|
|
3311 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3312 1 thread(s)
|
|
|
3313
|
|
|
3314
|
|
|
3315 Strategy:
|
|
|
3316 FFT-NS-i (Standard)
|
|
|
3317 Iterative refinement method (max. 1 iterations)
|
|
|
3318
|
|
|
3319 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3320 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3321
|
|
|
3322 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3323 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3324 To disable this change, add the --leavegappyregion option.
|
|
|
3325
|
|
|
3326 inputfile = orig
|
|
|
3327 6 x 106 - 87 d
|
|
|
3328 nthread = 1
|
|
|
3329 nthreadpair = 1
|
|
|
3330 nthreadtb = 1
|
|
|
3331 ppenalty_ex = 0
|
|
|
3332 stacksize: 8192 kb
|
|
|
3333 nsubalignments = 2
|
|
|
3334 maxmem = 4
|
|
|
3335 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3336 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3337
|
|
|
3338
|
|
|
3339
|
|
|
3340 Making a distance matrix ..
|
|
|
3341
1 / 6 (thread 0)
|
|
|
3342 done.
|
|
|
3343
|
|
|
3344 Constructing a UPGMA tree ...
|
|
|
3345
|
|
|
3346
0 / 6
|
|
|
3347 done.
|
|
|
3348
|
|
|
3349 Checking subalignment 1:
|
|
|
3350 -> OK
|
|
|
3351 Checking subalignment 2:
|
|
|
3352 -> OK
|
|
|
3353 Progressive alignment 1/2...
|
|
|
3354
STEP 5 / 5 (thread 0) f
|
|
|
3355 done.
|
|
|
3356
|
|
|
3357 Making a distance matrix from msa..
|
|
|
3358
0 / 6 (thread 0)
|
|
|
3359 done.
|
|
|
3360
|
|
|
3361 Constructing a UPGMA tree ...
|
|
|
3362
|
|
|
3363
0 / 6
|
|
|
3364 done.
|
|
|
3365
|
|
|
3366 Checking subalignment 1:
|
|
|
3367 -> OK
|
|
|
3368 Checking subalignment 2:
|
|
|
3369 -> OK
|
|
|
3370 Progressive alignment 2/2...
|
|
|
3371
STEP 5 / 5 (thread 0) f
|
|
|
3372 done.
|
|
|
3373
|
|
|
3374 disttbfast (nuc) Version 7.407
|
|
|
3375 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3376 1 thread(s)
|
|
|
3377
|
|
|
3378 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3379
0 / 6 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3380 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3381 1 thread(s)
|
|
|
3382
|
|
|
3383 minimumweight = 0.000010
|
|
|
3384 autosubalignment = 0.000000
|
|
|
3385 nthread = 1
|
|
|
3386 randomseed = 0
|
|
|
3387 blosum 62 / kimura 200
|
|
|
3388 poffset = 0
|
|
|
3389 niter = 1
|
|
|
3390 sueff_global = 0.100000
|
|
|
3391 nadd = 1
|
|
|
3392 nsubalignments = 2
|
|
|
3393 maxmem = 4
|
|
|
3394 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3395
|
|
|
3396
|
|
|
3397
0 / 6
|
|
|
3398
|
|
|
3399 Checking subalignment 1:
|
|
|
3400 1 2
|
|
|
3401 -> OK
|
|
|
3402
|
|
|
3403 Checking subalignment 2:
|
|
|
3404 3 4 5 6
|
|
|
3405 -> OK
|
|
|
3406 Segment 1/ 1 1- 127
|
|
|
3407 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-1 (thread 1) identical
001-0008-1 (thread 1) better
|
|
|
3408 Reached 1
|
|
|
3409 done
|
|
|
3410 dvtditr (nuc) Version 7.407
|
|
|
3411 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3412 1 thread(s)
|
|
|
3413
|
|
|
3414
|
|
|
3415 Strategy:
|
|
|
3416 FFT-NS-i (Standard)
|
|
|
3417 Iterative refinement method (max. 1 iterations)
|
|
|
3418
|
|
|
3419 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3420 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3421
|
|
|
3422 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3423 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3424 To disable this change, add the --leavegappyregion option.
|
|
|
3425
|
|
|
3426 inputfile = orig
|
|
|
3427 8 x 101 - 91 d
|
|
|
3428 nthread = 1
|
|
|
3429 nthreadpair = 1
|
|
|
3430 nthreadtb = 1
|
|
|
3431 ppenalty_ex = 0
|
|
|
3432 stacksize: 8192 kb
|
|
|
3433 nsubalignments = 2
|
|
|
3434 maxmem = 5
|
|
|
3435 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3436 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3437
|
|
|
3438
|
|
|
3439
|
|
|
3440 Making a distance matrix ..
|
|
|
3441
1 / 8 (thread 0)
|
|
|
3442 done.
|
|
|
3443
|
|
|
3444 Constructing a UPGMA tree ...
|
|
|
3445
|
|
|
3446
0 / 8
|
|
|
3447 done.
|
|
|
3448
|
|
|
3449 Checking subalignment 1:
|
|
|
3450 -> OK
|
|
|
3451 Checking subalignment 2:
|
|
|
3452 -> OK
|
|
|
3453 Progressive alignment 1/2...
|
|
|
3454
STEP 7 / 7 (thread 0) f
|
|
|
3455 done.
|
|
|
3456
|
|
|
3457 Making a distance matrix from msa..
|
|
|
3458
0 / 8 (thread 0)
|
|
|
3459 done.
|
|
|
3460
|
|
|
3461 Constructing a UPGMA tree ...
|
|
|
3462
|
|
|
3463
0 / 8
|
|
|
3464 done.
|
|
|
3465
|
|
|
3466 Checking subalignment 1:
|
|
|
3467 -> OK
|
|
|
3468 Checking subalignment 2:
|
|
|
3469 -> OK
|
|
|
3470 Progressive alignment 2/2...
|
|
|
3471
STEP 7 / 7 (thread 0) f
|
|
|
3472 done.
|
|
|
3473
|
|
|
3474 disttbfast (nuc) Version 7.407
|
|
|
3475 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3476 1 thread(s)
|
|
|
3477
|
|
|
3478 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3479
0 / 8 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3480 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3481 1 thread(s)
|
|
|
3482
|
|
|
3483 minimumweight = 0.000010
|
|
|
3484 autosubalignment = 0.000000
|
|
|
3485 nthread = 1
|
|
|
3486 randomseed = 0
|
|
|
3487 blosum 62 / kimura 200
|
|
|
3488 poffset = 0
|
|
|
3489 niter = 1
|
|
|
3490 sueff_global = 0.100000
|
|
|
3491 nadd = 1
|
|
|
3492 nsubalignments = 2
|
|
|
3493 maxmem = 5
|
|
|
3494 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3495
|
|
|
3496
|
|
|
3497
0 / 8
|
|
|
3498
|
|
|
3499 Checking subalignment 1:
|
|
|
3500 1 2 3 4 5
|
|
|
3501 -> OK
|
|
|
3502
|
|
|
3503 Checking subalignment 2:
|
|
|
3504 6 7 8
|
|
|
3505 -> OK
|
|
|
3506 Segment 1/ 1 1- 102
|
|
|
3507 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-1 (thread 1) identical
001-0012-1 (thread 1) worse
|
|
|
3508 Converged.
|
|
|
3509
|
|
|
3510 Reached 1
|
|
|
3511 done
|
|
|
3512 dvtditr (nuc) Version 7.407
|
|
|
3513 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3514 1 thread(s)
|
|
|
3515
|
|
|
3516
|
|
|
3517 Strategy:
|
|
|
3518 FFT-NS-i (Standard)
|
|
|
3519 Iterative refinement method (max. 1 iterations)
|
|
|
3520
|
|
|
3521 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3522 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3523
|
|
|
3524 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3525 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3526 To disable this change, add the --leavegappyregion option.
|
|
|
3527
|
|
|
3528 inputfile = orig
|
|
|
3529 6 x 99 - 85 d
|
|
|
3530 nthread = 1
|
|
|
3531 nthreadpair = 1
|
|
|
3532 nthreadtb = 1
|
|
|
3533 ppenalty_ex = 0
|
|
|
3534 stacksize: 8192 kb
|
|
|
3535 nsubalignments = 2
|
|
|
3536 maxmem = 4
|
|
|
3537 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3538 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3539
|
|
|
3540
|
|
|
3541
|
|
|
3542 Making a distance matrix ..
|
|
|
3543
1 / 6 (thread 0)
|
|
|
3544 done.
|
|
|
3545
|
|
|
3546 Constructing a UPGMA tree ...
|
|
|
3547
|
|
|
3548
0 / 6
|
|
|
3549 ###################################################################
|
|
|
3550 # WARNING: Group 2 is forced to be a monophyletic cluster.
|
|
|
3551 ###################################################################
|
|
|
3552 Reallocated inconsistentpairlist, size=2
|
|
|
3553
|
|
|
3554 done.
|
|
|
3555
|
|
|
3556 Checking subalignment 1:
|
|
|
3557 -> OK
|
|
|
3558 Checking subalignment 2:
|
|
|
3559 -> OK
|
|
|
3560 Progressive alignment 1/2...
|
|
|
3561
STEP 5 / 5 (thread 0) f
|
|
|
3562 done.
|
|
|
3563
|
|
|
3564 Making a distance matrix from msa..
|
|
|
3565
0 / 6 (thread 0)
|
|
|
3566 done.
|
|
|
3567
|
|
|
3568 Constructing a UPGMA tree ...
|
|
|
3569
|
|
|
3570
0 / 6
|
|
|
3571 done.
|
|
|
3572
|
|
|
3573 Checking subalignment 1:
|
|
|
3574 -> OK
|
|
|
3575 Checking subalignment 2:
|
|
|
3576 -> OK
|
|
|
3577 Progressive alignment 2/2...
|
|
|
3578
STEP 5 / 5 (thread 0) f
|
|
|
3579 done.
|
|
|
3580
|
|
|
3581 disttbfast (nuc) Version 7.407
|
|
|
3582 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3583 1 thread(s)
|
|
|
3584
|
|
|
3585 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3586
0 / 6 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3587 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3588 1 thread(s)
|
|
|
3589
|
|
|
3590 minimumweight = 0.000010
|
|
|
3591 autosubalignment = 0.000000
|
|
|
3592 nthread = 1
|
|
|
3593 randomseed = 0
|
|
|
3594 blosum 62 / kimura 200
|
|
|
3595 poffset = 0
|
|
|
3596 niter = 1
|
|
|
3597 sueff_global = 0.100000
|
|
|
3598 nadd = 1
|
|
|
3599 nsubalignments = 2
|
|
|
3600 maxmem = 4
|
|
|
3601 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3602
|
|
|
3603
|
|
|
3604
0 / 6
|
|
|
3605
|
|
|
3606 Checking subalignment 1:
|
|
|
3607 1 2
|
|
|
3608 -> OK
|
|
|
3609
|
|
|
3610 Checking subalignment 2:
|
|
|
3611 3 4 5 6
|
|
|
3612 -> OK
|
|
|
3613 Segment 1/ 1 1- 123
|
|
|
3614 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-1 (thread 1) identical
001-0008-1 (thread 1) better
|
|
|
3615 Reached 1
|
|
|
3616 done
|
|
|
3617 dvtditr (nuc) Version 7.407
|
|
|
3618 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3619 1 thread(s)
|
|
|
3620
|
|
|
3621
|
|
|
3622 Strategy:
|
|
|
3623 FFT-NS-i (Standard)
|
|
|
3624 Iterative refinement method (max. 1 iterations)
|
|
|
3625
|
|
|
3626 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3627 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3628
|
|
|
3629 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3630 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3631 To disable this change, add the --leavegappyregion option.
|
|
|
3632
|
|
|
3633 inputfile = orig
|
|
|
3634 6 x 115 - 94 d
|
|
|
3635 nthread = 1
|
|
|
3636 nthreadpair = 1
|
|
|
3637 nthreadtb = 1
|
|
|
3638 ppenalty_ex = 0
|
|
|
3639 stacksize: 8192 kb
|
|
|
3640 nsubalignments = 2
|
|
|
3641 maxmem = 4
|
|
|
3642 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3643 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3644
|
|
|
3645
|
|
|
3646
|
|
|
3647 Making a distance matrix ..
|
|
|
3648
1 / 6 (thread 0)
|
|
|
3649 done.
|
|
|
3650
|
|
|
3651 Constructing a UPGMA tree ...
|
|
|
3652
|
|
|
3653
0 / 6
|
|
|
3654 done.
|
|
|
3655
|
|
|
3656 Checking subalignment 1:
|
|
|
3657 -> OK
|
|
|
3658 Checking subalignment 2:
|
|
|
3659 -> OK
|
|
|
3660 Progressive alignment 1/2...
|
|
|
3661
STEP 5 / 5 (thread 0) f
|
|
|
3662 done.
|
|
|
3663
|
|
|
3664 Making a distance matrix from msa..
|
|
|
3665
0 / 6 (thread 0)
|
|
|
3666 done.
|
|
|
3667
|
|
|
3668 Constructing a UPGMA tree ...
|
|
|
3669
|
|
|
3670
0 / 6
|
|
|
3671 done.
|
|
|
3672
|
|
|
3673 Checking subalignment 1:
|
|
|
3674 -> OK
|
|
|
3675 Checking subalignment 2:
|
|
|
3676 -> OK
|
|
|
3677 Progressive alignment 2/2...
|
|
|
3678
STEP 5 / 5 (thread 0) f
|
|
|
3679 done.
|
|
|
3680
|
|
|
3681 disttbfast (nuc) Version 7.407
|
|
|
3682 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3683 1 thread(s)
|
|
|
3684
|
|
|
3685 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3686
0 / 6 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3687 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3688 1 thread(s)
|
|
|
3689
|
|
|
3690 minimumweight = 0.000010
|
|
|
3691 autosubalignment = 0.000000
|
|
|
3692 nthread = 1
|
|
|
3693 randomseed = 0
|
|
|
3694 blosum 62 / kimura 200
|
|
|
3695 poffset = 0
|
|
|
3696 niter = 1
|
|
|
3697 sueff_global = 0.100000
|
|
|
3698 nadd = 1
|
|
|
3699 nsubalignments = 2
|
|
|
3700 maxmem = 4
|
|
|
3701 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3702
|
|
|
3703
|
|
|
3704
0 / 6
|
|
|
3705
|
|
|
3706 Checking subalignment 1:
|
|
|
3707 1 2 3 4
|
|
|
3708 -> OK
|
|
|
3709
|
|
|
3710 Checking subalignment 2:
|
|
|
3711 5 6
|
|
|
3712 -> OK
|
|
|
3713 Segment 1/ 1 1- 141
|
|
|
3714 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-1 (thread 1) identical
|
|
|
3715 Converged.
|
|
|
3716
|
|
|
3717 Reached 1
|
|
|
3718 done
|
|
|
3719 dvtditr (nuc) Version 7.407
|
|
|
3720 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3721 1 thread(s)
|
|
|
3722
|
|
|
3723
|
|
|
3724 Strategy:
|
|
|
3725 FFT-NS-i (Standard)
|
|
|
3726 Iterative refinement method (max. 1 iterations)
|
|
|
3727
|
|
|
3728 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3729 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3730
|
|
|
3731 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3732 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3733 To disable this change, add the --leavegappyregion option.
|
|
|
3734
|
|
|
3735 inputfile = orig
|
|
|
3736 7 x 120 - 70 d
|
|
|
3737 nadd = 1
|
|
|
3738 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3739
0 / 6 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3740 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3741 1 thread(s)
|
|
|
3742
|
|
|
3743 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3744 All-to-all alignment.
|
|
|
3745
|
|
|
3746
|
|
|
3747 ##### writing hat3
|
|
|
3748 pairlocalalign (nuc) Version 7.407
|
|
|
3749 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3750 1 thread(s)
|
|
|
3751
|
|
|
3752 nadd = 1
|
|
|
3753 ppenalty_ex = -10
|
|
|
3754 nthread = 1
|
|
|
3755 blosum 62 / kimura 200
|
|
|
3756 sueff_global = 0.100000
|
|
|
3757 norg = 6
|
|
|
3758 njobc = 7
|
|
|
3759 Loading 'hat3' ...
|
|
|
3760 done.
|
|
|
3761 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3762 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
3763 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
3764
0 / 1 (thread 0)
c
|
|
|
3765
|
|
|
3766 Combining ..
|
|
|
3767 0 / 1
0 / 1
done.
|
|
|
3768
|
|
|
3769
done.
|
|
|
3770
|
|
|
3771 addsingle (nuc) Version 7.407
|
|
|
3772 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3773 1 thread(s)
|
|
|
3774
|
|
|
3775
|
|
|
3776 Strategy:
|
|
|
3777 Multi-INS-fragment (Not tested.)
|
|
|
3778 ?
|
|
|
3779
|
|
|
3780 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3781 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3782
|
|
|
3783 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3784 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3785 To disable this change, add the --leavegappyregion option.
|
|
|
3786
|
|
|
3787 inputfile = orig
|
|
|
3788 6 x 99 - 70 d
|
|
|
3789 nadd = 1
|
|
|
3790 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3791
0 / 5 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3792 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3793 1 thread(s)
|
|
|
3794
|
|
|
3795 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3796 All-to-all alignment.
|
|
|
3797
|
|
|
3798
|
|
|
3799 ##### writing hat3
|
|
|
3800 pairlocalalign (nuc) Version 7.407
|
|
|
3801 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3802 1 thread(s)
|
|
|
3803
|
|
|
3804 nadd = 1
|
|
|
3805 ppenalty_ex = -10
|
|
|
3806 nthread = 1
|
|
|
3807 blosum 62 / kimura 200
|
|
|
3808 sueff_global = 0.100000
|
|
|
3809 norg = 5
|
|
|
3810 njobc = 6
|
|
|
3811 Loading 'hat3' ...
|
|
|
3812 done.
|
|
|
3813 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3814 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
3815 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
3816
0 / 1 (thread 0)
c
|
|
|
3817
|
|
|
3818 Combining ..
|
|
|
3819 0 / 1
0 / 1
done.
|
|
|
3820
|
|
|
3821
done.
|
|
|
3822
|
|
|
3823 addsingle (nuc) Version 7.407
|
|
|
3824 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3825 1 thread(s)
|
|
|
3826
|
|
|
3827
|
|
|
3828 Strategy:
|
|
|
3829 Multi-INS-fragment (Not tested.)
|
|
|
3830 ?
|
|
|
3831
|
|
|
3832 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3833 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3834
|
|
|
3835 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3836 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3837 To disable this change, add the --leavegappyregion option.
|
|
|
3838
|
|
|
3839 inputfile = orig
|
|
|
3840 9 x 104 - 70 d
|
|
|
3841 nadd = 1
|
|
|
3842 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3843
0 / 8 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3844 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3845 1 thread(s)
|
|
|
3846
|
|
|
3847 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3848 All-to-all alignment.
|
|
|
3849
|
|
|
3850
|
|
|
3851 ##### writing hat3
|
|
|
3852 pairlocalalign (nuc) Version 7.407
|
|
|
3853 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3854 1 thread(s)
|
|
|
3855
|
|
|
3856 nadd = 1
|
|
|
3857 ppenalty_ex = -10
|
|
|
3858 nthread = 1
|
|
|
3859 blosum 62 / kimura 200
|
|
|
3860 sueff_global = 0.100000
|
|
|
3861 norg = 8
|
|
|
3862 njobc = 9
|
|
|
3863 Loading 'hat3' ...
|
|
|
3864 done.
|
|
|
3865 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3866 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
3867 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
3868
0 / 1 (thread 0)
c
|
|
|
3869
|
|
|
3870 Combining ..
|
|
|
3871 0 / 1
0 / 1
done.
|
|
|
3872
|
|
|
3873
done.
|
|
|
3874
|
|
|
3875 addsingle (nuc) Version 7.407
|
|
|
3876 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3877 1 thread(s)
|
|
|
3878
|
|
|
3879
|
|
|
3880 Strategy:
|
|
|
3881 Multi-INS-fragment (Not tested.)
|
|
|
3882 ?
|
|
|
3883
|
|
|
3884 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3885 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3886
|
|
|
3887 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3888 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3889 To disable this change, add the --leavegappyregion option.
|
|
|
3890
|
|
|
3891 inputfile = orig
|
|
|
3892 6 x 108 - 70 d
|
|
|
3893 nadd = 1
|
|
|
3894 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3895
0 / 5 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3896 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3897 1 thread(s)
|
|
|
3898
|
|
|
3899 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3900 All-to-all alignment.
|
|
|
3901
|
|
|
3902
|
|
|
3903 ##### writing hat3
|
|
|
3904 pairlocalalign (nuc) Version 7.407
|
|
|
3905 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
3906 1 thread(s)
|
|
|
3907
|
|
|
3908 nadd = 1
|
|
|
3909 ppenalty_ex = -10
|
|
|
3910 nthread = 1
|
|
|
3911 blosum 62 / kimura 200
|
|
|
3912 sueff_global = 0.100000
|
|
|
3913 norg = 5
|
|
|
3914 njobc = 6
|
|
|
3915 Loading 'hat3' ...
|
|
|
3916 done.
|
|
|
3917 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3918 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
3919 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
3920
0 / 1 (thread 0)
c
|
|
|
3921
|
|
|
3922 Combining ..
|
|
|
3923 0 / 1
0 / 1
done.
|
|
|
3924
|
|
|
3925
done.
|
|
|
3926
|
|
|
3927 addsingle (nuc) Version 7.407
|
|
|
3928 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3929 1 thread(s)
|
|
|
3930
|
|
|
3931
|
|
|
3932 Strategy:
|
|
|
3933 Multi-INS-fragment (Not tested.)
|
|
|
3934 ?
|
|
|
3935
|
|
|
3936 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
3937 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
3938
|
|
|
3939 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
3940 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
3941 To disable this change, add the --leavegappyregion option.
|
|
|
3942
|
|
|
3943 inputfile = orig
|
|
|
3944 8 x 126 - 83 d
|
|
|
3945 nthread = 1
|
|
|
3946 nthreadpair = 1
|
|
|
3947 nthreadtb = 1
|
|
|
3948 ppenalty_ex = 0
|
|
|
3949 stacksize: 8192 kb
|
|
|
3950 nsubalignments = 2
|
|
|
3951 maxmem = 6
|
|
|
3952 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3953 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
3954
|
|
|
3955
|
|
|
3956
|
|
|
3957 Making a distance matrix ..
|
|
|
3958
1 / 8 (thread 0)
|
|
|
3959 done.
|
|
|
3960
|
|
|
3961 Constructing a UPGMA tree ...
|
|
|
3962
|
|
|
3963
0 / 8
|
|
|
3964 done.
|
|
|
3965
|
|
|
3966 Checking subalignment 1:
|
|
|
3967 -> OK
|
|
|
3968 Checking subalignment 2:
|
|
|
3969 -> OK
|
|
|
3970 Progressive alignment 1/2...
|
|
|
3971
STEP 7 / 7 (thread 0) f
|
|
|
3972 done.
|
|
|
3973
|
|
|
3974 Making a distance matrix from msa..
|
|
|
3975
0 / 8 (thread 0)
|
|
|
3976 done.
|
|
|
3977
|
|
|
3978 Constructing a UPGMA tree ...
|
|
|
3979
|
|
|
3980
0 / 8
|
|
|
3981 done.
|
|
|
3982
|
|
|
3983 Checking subalignment 1:
|
|
|
3984 -> OK
|
|
|
3985 Checking subalignment 2:
|
|
|
3986 -> OK
|
|
|
3987 Progressive alignment 2/2...
|
|
|
3988
STEP 7 / 7 (thread 0) f
|
|
|
3989 done.
|
|
|
3990
|
|
|
3991 disttbfast (nuc) Version 7.407
|
|
|
3992 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
3993 1 thread(s)
|
|
|
3994
|
|
|
3995 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
3996
0 / 8 (thread 0)dndpre (nuc) Version 7.407
|
|
|
3997 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
3998 1 thread(s)
|
|
|
3999
|
|
|
4000 minimumweight = 0.000010
|
|
|
4001 autosubalignment = 0.000000
|
|
|
4002 nthread = 1
|
|
|
4003 randomseed = 0
|
|
|
4004 blosum 62 / kimura 200
|
|
|
4005 poffset = 0
|
|
|
4006 niter = 1
|
|
|
4007 sueff_global = 0.100000
|
|
|
4008 nadd = 1
|
|
|
4009 nsubalignments = 2
|
|
|
4010 maxmem = 6
|
|
|
4011 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4012
|
|
|
4013
|
|
|
4014
0 / 8
|
|
|
4015
|
|
|
4016 Checking subalignment 1:
|
|
|
4017 1 2
|
|
|
4018 -> OK
|
|
|
4019
|
|
|
4020 Checking subalignment 2:
|
|
|
4021 3 4 5 6 7 8
|
|
|
4022 -> OK
|
|
|
4023 Segment 1/ 1 1- 130
|
|
|
4024 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-1 (thread 1) identical
001-0012-1 (thread 1) better
|
|
|
4025 Reached 1
|
|
|
4026 done
|
|
|
4027 dvtditr (nuc) Version 7.407
|
|
|
4028 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4029 1 thread(s)
|
|
|
4030
|
|
|
4031
|
|
|
4032 Strategy:
|
|
|
4033 FFT-NS-i (Standard)
|
|
|
4034 Iterative refinement method (max. 1 iterations)
|
|
|
4035
|
|
|
4036 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4037 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4038
|
|
|
4039 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4040 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4041 To disable this change, add the --leavegappyregion option.
|
|
|
4042
|
|
|
4043 inputfile = orig
|
|
|
4044 7 x 100 - 70 d
|
|
|
4045 nadd = 1
|
|
|
4046 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4047
0 / 6 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4048 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4049 1 thread(s)
|
|
|
4050
|
|
|
4051 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4052 All-to-all alignment.
|
|
|
4053
|
|
|
4054
|
|
|
4055 ##### writing hat3
|
|
|
4056 pairlocalalign (nuc) Version 7.407
|
|
|
4057 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4058 1 thread(s)
|
|
|
4059
|
|
|
4060 nadd = 1
|
|
|
4061 ppenalty_ex = -10
|
|
|
4062 nthread = 1
|
|
|
4063 blosum 62 / kimura 200
|
|
|
4064 sueff_global = 0.100000
|
|
|
4065 norg = 6
|
|
|
4066 njobc = 7
|
|
|
4067 Loading 'hat3' ...
|
|
|
4068 done.
|
|
|
4069 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4070 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
4071 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
4072
0 / 1 (thread 0)
c
|
|
|
4073
|
|
|
4074 Combining ..
|
|
|
4075 0 / 1
0 / 1
done.
|
|
|
4076
|
|
|
4077
done.
|
|
|
4078
|
|
|
4079 addsingle (nuc) Version 7.407
|
|
|
4080 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4081 1 thread(s)
|
|
|
4082
|
|
|
4083
|
|
|
4084 Strategy:
|
|
|
4085 Multi-INS-fragment (Not tested.)
|
|
|
4086 ?
|
|
|
4087
|
|
|
4088 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4089 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4090
|
|
|
4091 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4092 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4093 To disable this change, add the --leavegappyregion option.
|
|
|
4094
|
|
|
4095 inputfile = orig
|
|
|
4096 7 x 140 - 70 d
|
|
|
4097 nadd = 1
|
|
|
4098 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4099
0 / 6 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4100 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4101 1 thread(s)
|
|
|
4102
|
|
|
4103 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4104 All-to-all alignment.
|
|
|
4105
|
|
|
4106
|
|
|
4107 ##### writing hat3
|
|
|
4108 pairlocalalign (nuc) Version 7.407
|
|
|
4109 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4110 1 thread(s)
|
|
|
4111
|
|
|
4112 nadd = 1
|
|
|
4113 ppenalty_ex = -10
|
|
|
4114 nthread = 1
|
|
|
4115 blosum 62 / kimura 200
|
|
|
4116 sueff_global = 0.100000
|
|
|
4117 norg = 6
|
|
|
4118 njobc = 7
|
|
|
4119 Loading 'hat3' ...
|
|
|
4120 done.
|
|
|
4121 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4122 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
4123 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
4124
0 / 1 (thread 0)
c
|
|
|
4125
|
|
|
4126 Combining ..
|
|
|
4127 0 / 1
0 / 1
done.
|
|
|
4128
|
|
|
4129
done.
|
|
|
4130
|
|
|
4131 addsingle (nuc) Version 7.407
|
|
|
4132 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4133 1 thread(s)
|
|
|
4134
|
|
|
4135
|
|
|
4136 Strategy:
|
|
|
4137 Multi-INS-fragment (Not tested.)
|
|
|
4138 ?
|
|
|
4139
|
|
|
4140 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4141 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4142
|
|
|
4143 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4144 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4145 To disable this change, add the --leavegappyregion option.
|
|
|
4146
|
|
|
4147 inputfile = orig
|
|
|
4148 13 x 128 - 123 d
|
|
|
4149 nthread = 1
|
|
|
4150 nthreadpair = 1
|
|
|
4151 nthreadtb = 1
|
|
|
4152 ppenalty_ex = 0
|
|
|
4153 stacksize: 8192 kb
|
|
|
4154 nsubalignments = 2
|
|
|
4155 maxmem = 7
|
|
|
4156 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4157 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4158
|
|
|
4159
|
|
|
4160
|
|
|
4161 Making a distance matrix ..
|
|
|
4162
1 / 13 (thread 0)
|
|
|
4163 done.
|
|
|
4164
|
|
|
4165 Constructing a UPGMA tree ...
|
|
|
4166
|
|
|
4167
0 / 13
10 / 13
|
|
|
4168 done.
|
|
|
4169
|
|
|
4170 Checking subalignment 1:
|
|
|
4171 -> OK
|
|
|
4172 Checking subalignment 2:
|
|
|
4173 -> OK
|
|
|
4174 Progressive alignment 1/2...
|
|
|
4175
STEP 12 / 12 (thread 0) f
|
|
|
4176 done.
|
|
|
4177
|
|
|
4178 Making a distance matrix from msa..
|
|
|
4179
0 / 13 (thread 0)
|
|
|
4180 done.
|
|
|
4181
|
|
|
4182 Constructing a UPGMA tree ...
|
|
|
4183
|
|
|
4184
0 / 13
10 / 13
|
|
|
4185 done.
|
|
|
4186
|
|
|
4187 Checking subalignment 1:
|
|
|
4188 -> OK
|
|
|
4189 Checking subalignment 2:
|
|
|
4190 -> OK
|
|
|
4191 Progressive alignment 2/2...
|
|
|
4192
STEP 12 / 12 (thread 0) f
|
|
|
4193 done.
|
|
|
4194
|
|
|
4195 disttbfast (nuc) Version 7.407
|
|
|
4196 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4197 1 thread(s)
|
|
|
4198
|
|
|
4199 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4200
0 / 13 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4201 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
4202 1 thread(s)
|
|
|
4203
|
|
|
4204 minimumweight = 0.000010
|
|
|
4205 autosubalignment = 0.000000
|
|
|
4206 nthread = 1
|
|
|
4207 randomseed = 0
|
|
|
4208 blosum 62 / kimura 200
|
|
|
4209 poffset = 0
|
|
|
4210 niter = 1
|
|
|
4211 sueff_global = 0.100000
|
|
|
4212 nadd = 1
|
|
|
4213 nsubalignments = 2
|
|
|
4214 maxmem = 7
|
|
|
4215 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4216
|
|
|
4217
|
|
|
4218
0 / 13
10 / 13
|
|
|
4219
|
|
|
4220 Checking subalignment 1:
|
|
|
4221 1 2 3 4 5 6
|
|
|
4222 -> OK
|
|
|
4223
|
|
|
4224 Checking subalignment 2:
|
|
|
4225 7 8 9 10 11 12 13
|
|
|
4226 -> OK
|
|
|
4227 Segment 1/ 1 1- 163
|
|
|
4228 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-1 (thread 1) identical
001-0022-1 (thread 1) better
|
|
|
4229 Reached 1
|
|
|
4230 done
|
|
|
4231 dvtditr (nuc) Version 7.407
|
|
|
4232 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4233 1 thread(s)
|
|
|
4234
|
|
|
4235
|
|
|
4236 Strategy:
|
|
|
4237 FFT-NS-i (Standard)
|
|
|
4238 Iterative refinement method (max. 1 iterations)
|
|
|
4239
|
|
|
4240 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4241 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4242
|
|
|
4243 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4244 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4245 To disable this change, add the --leavegappyregion option.
|
|
|
4246
|
|
|
4247 inputfile = orig
|
|
|
4248 10 x 130 - 111 d
|
|
|
4249 nthread = 1
|
|
|
4250 nthreadpair = 1
|
|
|
4251 nthreadtb = 1
|
|
|
4252 ppenalty_ex = 0
|
|
|
4253 stacksize: 8192 kb
|
|
|
4254 nsubalignments = 2
|
|
|
4255 maxmem = 6
|
|
|
4256 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4257 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4258
|
|
|
4259
|
|
|
4260
|
|
|
4261 Making a distance matrix ..
|
|
|
4262
1 / 10 (thread 0)
|
|
|
4263 done.
|
|
|
4264
|
|
|
4265 Constructing a UPGMA tree ...
|
|
|
4266
|
|
|
4267
0 / 10
|
|
|
4268 done.
|
|
|
4269
|
|
|
4270 Checking subalignment 1:
|
|
|
4271 -> OK
|
|
|
4272 Checking subalignment 2:
|
|
|
4273 -> OK
|
|
|
4274 Progressive alignment 1/2...
|
|
|
4275
STEP 9 / 9 (thread 0) f
|
|
|
4276 done.
|
|
|
4277
|
|
|
4278 Making a distance matrix from msa..
|
|
|
4279
0 / 10 (thread 0)
|
|
|
4280 done.
|
|
|
4281
|
|
|
4282 Constructing a UPGMA tree ...
|
|
|
4283
|
|
|
4284
0 / 10
|
|
|
4285 done.
|
|
|
4286
|
|
|
4287 Checking subalignment 1:
|
|
|
4288 -> OK
|
|
|
4289 Checking subalignment 2:
|
|
|
4290 -> OK
|
|
|
4291 Progressive alignment 2/2...
|
|
|
4292
STEP 9 / 9 (thread 0) f
|
|
|
4293 done.
|
|
|
4294
|
|
|
4295 disttbfast (nuc) Version 7.407
|
|
|
4296 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4297 1 thread(s)
|
|
|
4298
|
|
|
4299 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4300
0 / 10 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4301 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
4302 1 thread(s)
|
|
|
4303
|
|
|
4304 minimumweight = 0.000010
|
|
|
4305 autosubalignment = 0.000000
|
|
|
4306 nthread = 1
|
|
|
4307 randomseed = 0
|
|
|
4308 blosum 62 / kimura 200
|
|
|
4309 poffset = 0
|
|
|
4310 niter = 1
|
|
|
4311 sueff_global = 0.100000
|
|
|
4312 nadd = 1
|
|
|
4313 nsubalignments = 2
|
|
|
4314 maxmem = 6
|
|
|
4315 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4316
|
|
|
4317
|
|
|
4318
0 / 10
|
|
|
4319
|
|
|
4320 Checking subalignment 1:
|
|
|
4321 1 2 3 4
|
|
|
4322 -> OK
|
|
|
4323
|
|
|
4324 Checking subalignment 2:
|
|
|
4325 5 6 7 8 9 10
|
|
|
4326 -> OK
|
|
|
4327 Segment 1/ 1 1- 142
|
|
|
4328 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-1 (thread 1) identical
|
|
|
4329 Converged.
|
|
|
4330
|
|
|
4331 Reached 1
|
|
|
4332 done
|
|
|
4333 dvtditr (nuc) Version 7.407
|
|
|
4334 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4335 1 thread(s)
|
|
|
4336
|
|
|
4337
|
|
|
4338 Strategy:
|
|
|
4339 FFT-NS-i (Standard)
|
|
|
4340 Iterative refinement method (max. 1 iterations)
|
|
|
4341
|
|
|
4342 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4343 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4344
|
|
|
4345 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4346 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4347 To disable this change, add the --leavegappyregion option.
|
|
|
4348
|
|
|
4349 inputfile = orig
|
|
|
4350 16 x 129 - 101 d
|
|
|
4351 nthread = 1
|
|
|
4352 nthreadpair = 1
|
|
|
4353 nthreadtb = 1
|
|
|
4354 ppenalty_ex = 0
|
|
|
4355 stacksize: 8192 kb
|
|
|
4356 nsubalignments = 2
|
|
|
4357 maxmem = 8
|
|
|
4358 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4359 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4360
|
|
|
4361
|
|
|
4362
|
|
|
4363 Making a distance matrix ..
|
|
|
4364
1 / 16 (thread 0)
|
|
|
4365 done.
|
|
|
4366
|
|
|
4367 Constructing a UPGMA tree ...
|
|
|
4368
|
|
|
4369
0 / 16
10 / 16
|
|
|
4370 done.
|
|
|
4371
|
|
|
4372 Checking subalignment 1:
|
|
|
4373 -> OK
|
|
|
4374 Checking subalignment 2:
|
|
|
4375 -> OK
|
|
|
4376 Progressive alignment 1/2...
|
|
|
4377
STEP 15 / 15 (thread 0) f
|
|
|
4378 done.
|
|
|
4379
|
|
|
4380 Making a distance matrix from msa..
|
|
|
4381
0 / 16 (thread 0)
|
|
|
4382 done.
|
|
|
4383
|
|
|
4384 Constructing a UPGMA tree ...
|
|
|
4385
|
|
|
4386
0 / 16
10 / 16
|
|
|
4387 done.
|
|
|
4388
|
|
|
4389 Checking subalignment 1:
|
|
|
4390 -> OK
|
|
|
4391 Checking subalignment 2:
|
|
|
4392 -> OK
|
|
|
4393 Progressive alignment 2/2...
|
|
|
4394
STEP 15 / 15 (thread 0) f
|
|
|
4395 done.
|
|
|
4396
|
|
|
4397 disttbfast (nuc) Version 7.407
|
|
|
4398 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4399 1 thread(s)
|
|
|
4400
|
|
|
4401 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4402
0 / 16 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4403 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
4404 1 thread(s)
|
|
|
4405
|
|
|
4406 minimumweight = 0.000010
|
|
|
4407 autosubalignment = 0.000000
|
|
|
4408 nthread = 1
|
|
|
4409 randomseed = 0
|
|
|
4410 blosum 62 / kimura 200
|
|
|
4411 poffset = 0
|
|
|
4412 niter = 1
|
|
|
4413 sueff_global = 0.100000
|
|
|
4414 nadd = 1
|
|
|
4415 nsubalignments = 2
|
|
|
4416 maxmem = 8
|
|
|
4417 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4418
|
|
|
4419
|
|
|
4420
0 / 16
10 / 16
|
|
|
4421
|
|
|
4422 Checking subalignment 1:
|
|
|
4423 1 2 3 4 5 6 7 8
|
|
|
4424 -> OK
|
|
|
4425
|
|
|
4426 Checking subalignment 2:
|
|
|
4427 9 10 11 12 13 14 15 16
|
|
|
4428 -> OK
|
|
|
4429 Segment 1/ 1 1- 152
|
|
|
4430 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-1 (thread 1) identical
001-0028-1 (thread 1) better
|
|
|
4431 Reached 1
|
|
|
4432 done
|
|
|
4433 dvtditr (nuc) Version 7.407
|
|
|
4434 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4435 1 thread(s)
|
|
|
4436
|
|
|
4437
|
|
|
4438 Strategy:
|
|
|
4439 FFT-NS-i (Standard)
|
|
|
4440 Iterative refinement method (max. 1 iterations)
|
|
|
4441
|
|
|
4442 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4443 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4444
|
|
|
4445 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4446 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4447 To disable this change, add the --leavegappyregion option.
|
|
|
4448
|
|
|
4449 inputfile = orig
|
|
|
4450 10 x 108 - 96 d
|
|
|
4451 nthread = 1
|
|
|
4452 nthreadpair = 1
|
|
|
4453 nthreadtb = 1
|
|
|
4454 ppenalty_ex = 0
|
|
|
4455 stacksize: 8192 kb
|
|
|
4456 nsubalignments = 2
|
|
|
4457 maxmem = 7
|
|
|
4458 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4459 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4460
|
|
|
4461
|
|
|
4462
|
|
|
4463 Making a distance matrix ..
|
|
|
4464
1 / 10 (thread 0)
|
|
|
4465 done.
|
|
|
4466
|
|
|
4467 Constructing a UPGMA tree ...
|
|
|
4468
|
|
|
4469
0 / 10
|
|
|
4470 done.
|
|
|
4471
|
|
|
4472 Checking subalignment 1:
|
|
|
4473 -> OK
|
|
|
4474 Checking subalignment 2:
|
|
|
4475 -> OK
|
|
|
4476 Progressive alignment 1/2...
|
|
|
4477
STEP 9 / 9 (thread 0) f
|
|
|
4478 done.
|
|
|
4479
|
|
|
4480 Making a distance matrix from msa..
|
|
|
4481
0 / 10 (thread 0)
|
|
|
4482 done.
|
|
|
4483
|
|
|
4484 Constructing a UPGMA tree ...
|
|
|
4485
|
|
|
4486
0 / 10
|
|
|
4487 done.
|
|
|
4488
|
|
|
4489 Checking subalignment 1:
|
|
|
4490 -> OK
|
|
|
4491 Checking subalignment 2:
|
|
|
4492 -> OK
|
|
|
4493 Progressive alignment 2/2...
|
|
|
4494
STEP 9 / 9 (thread 0) f
|
|
|
4495 done.
|
|
|
4496
|
|
|
4497 disttbfast (nuc) Version 7.407
|
|
|
4498 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4499 1 thread(s)
|
|
|
4500
|
|
|
4501 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4502
0 / 10 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4503 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
4504 1 thread(s)
|
|
|
4505
|
|
|
4506 minimumweight = 0.000010
|
|
|
4507 autosubalignment = 0.000000
|
|
|
4508 nthread = 1
|
|
|
4509 randomseed = 0
|
|
|
4510 blosum 62 / kimura 200
|
|
|
4511 poffset = 0
|
|
|
4512 niter = 1
|
|
|
4513 sueff_global = 0.100000
|
|
|
4514 nadd = 1
|
|
|
4515 nsubalignments = 2
|
|
|
4516 maxmem = 7
|
|
|
4517 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4518
|
|
|
4519
|
|
|
4520
0 / 10
|
|
|
4521
|
|
|
4522 Checking subalignment 1:
|
|
|
4523 1 2 3
|
|
|
4524 -> OK
|
|
|
4525
|
|
|
4526 Checking subalignment 2:
|
|
|
4527 4 5 6 7 8 9 10
|
|
|
4528 -> OK
|
|
|
4529 Segment 1/ 1 1- 122
|
|
|
4530 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-1 (thread 1) identical
001-0016-1 (thread 1) better
|
|
|
4531 Reached 1
|
|
|
4532 done
|
|
|
4533 dvtditr (nuc) Version 7.407
|
|
|
4534 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4535 1 thread(s)
|
|
|
4536
|
|
|
4537
|
|
|
4538 Strategy:
|
|
|
4539 FFT-NS-i (Standard)
|
|
|
4540 Iterative refinement method (max. 1 iterations)
|
|
|
4541
|
|
|
4542 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4543 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4544
|
|
|
4545 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4546 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4547 To disable this change, add the --leavegappyregion option.
|
|
|
4548
|
|
|
4549 inputfile = orig
|
|
|
4550 8 x 140 - 70 d
|
|
|
4551 nadd = 1
|
|
|
4552 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4553
0 / 7 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4554 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4555 1 thread(s)
|
|
|
4556
|
|
|
4557 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4558 All-to-all alignment.
|
|
|
4559
|
|
|
4560
|
|
|
4561 ##### writing hat3
|
|
|
4562 pairlocalalign (nuc) Version 7.407
|
|
|
4563 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4564 1 thread(s)
|
|
|
4565
|
|
|
4566 nadd = 1
|
|
|
4567 ppenalty_ex = -10
|
|
|
4568 nthread = 1
|
|
|
4569 blosum 62 / kimura 200
|
|
|
4570 sueff_global = 0.100000
|
|
|
4571 norg = 7
|
|
|
4572 njobc = 8
|
|
|
4573 Loading 'hat3' ...
|
|
|
4574 done.
|
|
|
4575 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4576 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
4577 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
4578
0 / 1 (thread 0)
c
|
|
|
4579
|
|
|
4580 Combining ..
|
|
|
4581 0 / 1
0 / 1
done.
|
|
|
4582
|
|
|
4583
done.
|
|
|
4584
|
|
|
4585 addsingle (nuc) Version 7.407
|
|
|
4586 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4587 1 thread(s)
|
|
|
4588
|
|
|
4589
|
|
|
4590 Strategy:
|
|
|
4591 Multi-INS-fragment (Not tested.)
|
|
|
4592 ?
|
|
|
4593
|
|
|
4594 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4595 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4596
|
|
|
4597 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4598 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4599 To disable this change, add the --leavegappyregion option.
|
|
|
4600
|
|
|
4601 inputfile = orig
|
|
|
4602 17 x 151 - 113 d
|
|
|
4603 nthread = 1
|
|
|
4604 nthreadpair = 1
|
|
|
4605 nthreadtb = 1
|
|
|
4606 ppenalty_ex = 0
|
|
|
4607 stacksize: 8192 kb
|
|
|
4608 nsubalignments = 2
|
|
|
4609 maxmem = 13
|
|
|
4610 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4611 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4612
|
|
|
4613
|
|
|
4614
|
|
|
4615 Making a distance matrix ..
|
|
|
4616
1 / 17 (thread 0)
|
|
|
4617 done.
|
|
|
4618
|
|
|
4619 Constructing a UPGMA tree ...
|
|
|
4620
|
|
|
4621
0 / 17
10 / 17
|
|
|
4622 done.
|
|
|
4623
|
|
|
4624 Checking subalignment 1:
|
|
|
4625 -> OK
|
|
|
4626 Checking subalignment 2:
|
|
|
4627 -> OK
|
|
|
4628 Progressive alignment 1/2...
|
|
|
4629
STEP 16 / 16 (thread 0) f
|
|
|
4630 done.
|
|
|
4631
|
|
|
4632 Making a distance matrix from msa..
|
|
|
4633
0 / 17 (thread 0)
|
|
|
4634 done.
|
|
|
4635
|
|
|
4636 Constructing a UPGMA tree ...
|
|
|
4637
|
|
|
4638
0 / 17
10 / 17
|
|
|
4639 done.
|
|
|
4640
|
|
|
4641 Checking subalignment 1:
|
|
|
4642 -> OK
|
|
|
4643 Checking subalignment 2:
|
|
|
4644 -> OK
|
|
|
4645 Progressive alignment 2/2...
|
|
|
4646
STEP 16 / 16 (thread 0) f
|
|
|
4647 done.
|
|
|
4648
|
|
|
4649 disttbfast (nuc) Version 7.407
|
|
|
4650 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4651 1 thread(s)
|
|
|
4652
|
|
|
4653 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4654
0 / 17 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4655 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
4656 1 thread(s)
|
|
|
4657
|
|
|
4658 minimumweight = 0.000010
|
|
|
4659 autosubalignment = 0.000000
|
|
|
4660 nthread = 1
|
|
|
4661 randomseed = 0
|
|
|
4662 blosum 62 / kimura 200
|
|
|
4663 poffset = 0
|
|
|
4664 niter = 1
|
|
|
4665 sueff_global = 0.100000
|
|
|
4666 nadd = 1
|
|
|
4667 nsubalignments = 2
|
|
|
4668 maxmem = 13
|
|
|
4669 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4670
|
|
|
4671
|
|
|
4672
0 / 17
10 / 17
|
|
|
4673
|
|
|
4674 Checking subalignment 1:
|
|
|
4675 1 2 3 4 5 6 7 8 9 10 11 12 13
|
|
|
4676 -> OK
|
|
|
4677
|
|
|
4678 Checking subalignment 2:
|
|
|
4679 14 15 16 17
|
|
|
4680 -> OK
|
|
|
4681 Segment 1/ 1 1- 166
|
|
|
4682 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-1 (thread 1) identical
001-0030-1 (thread 1) better
|
|
|
4683 Reached 1
|
|
|
4684 done
|
|
|
4685 dvtditr (nuc) Version 7.407
|
|
|
4686 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4687 1 thread(s)
|
|
|
4688
|
|
|
4689
|
|
|
4690 Strategy:
|
|
|
4691 FFT-NS-i (Standard)
|
|
|
4692 Iterative refinement method (max. 1 iterations)
|
|
|
4693
|
|
|
4694 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4695 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4696
|
|
|
4697 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4698 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4699 To disable this change, add the --leavegappyregion option.
|
|
|
4700
|
|
|
4701 inputfile = orig
|
|
|
4702 11 x 141 - 70 d
|
|
|
4703 nadd = 1
|
|
|
4704 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4705
0 / 10 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4706 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4707 1 thread(s)
|
|
|
4708
|
|
|
4709 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4710 All-to-all alignment.
|
|
|
4711
|
|
|
4712
|
|
|
4713 ##### writing hat3
|
|
|
4714 pairlocalalign (nuc) Version 7.407
|
|
|
4715 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
4716 1 thread(s)
|
|
|
4717
|
|
|
4718 nadd = 1
|
|
|
4719 ppenalty_ex = -10
|
|
|
4720 nthread = 1
|
|
|
4721 blosum 62 / kimura 200
|
|
|
4722 sueff_global = 0.100000
|
|
|
4723 norg = 10
|
|
|
4724 njobc = 11
|
|
|
4725 Loading 'hat3' ...
|
|
|
4726 done.
|
|
|
4727 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4728 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
4729 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
4730
0 / 1 (thread 0)
c
|
|
|
4731
|
|
|
4732 Combining ..
|
|
|
4733 0 / 1
0 / 1
done.
|
|
|
4734
|
|
|
4735
done.
|
|
|
4736
|
|
|
4737 addsingle (nuc) Version 7.407
|
|
|
4738 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4739 1 thread(s)
|
|
|
4740
|
|
|
4741
|
|
|
4742 Strategy:
|
|
|
4743 Multi-INS-fragment (Not tested.)
|
|
|
4744 ?
|
|
|
4745
|
|
|
4746 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4747 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4748
|
|
|
4749 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4750 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4751 To disable this change, add the --leavegappyregion option.
|
|
|
4752
|
|
|
4753 inputfile = orig
|
|
|
4754 22 x 157 - 112 d
|
|
|
4755 nthread = 1
|
|
|
4756 nthreadpair = 1
|
|
|
4757 nthreadtb = 1
|
|
|
4758 ppenalty_ex = 0
|
|
|
4759 stacksize: 8192 kb
|
|
|
4760 nsubalignments = 2
|
|
|
4761 maxmem = 16
|
|
|
4762 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4763 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4764
|
|
|
4765
|
|
|
4766
|
|
|
4767 Making a distance matrix ..
|
|
|
4768
1 / 22 (thread 0)
|
|
|
4769 done.
|
|
|
4770
|
|
|
4771 Constructing a UPGMA tree ...
|
|
|
4772
|
|
|
4773
0 / 22
10 / 22
20 / 22
|
|
|
4774 done.
|
|
|
4775
|
|
|
4776 Checking subalignment 1:
|
|
|
4777 -> OK
|
|
|
4778 Checking subalignment 2:
|
|
|
4779 -> OK
|
|
|
4780 Progressive alignment 1/2...
|
|
|
4781
STEP 21 / 21 (thread 0) f
|
|
|
4782 done.
|
|
|
4783
|
|
|
4784 Making a distance matrix from msa..
|
|
|
4785
0 / 22 (thread 0)
|
|
|
4786 done.
|
|
|
4787
|
|
|
4788 Constructing a UPGMA tree ...
|
|
|
4789
|
|
|
4790
0 / 22
10 / 22
20 / 22
|
|
|
4791 done.
|
|
|
4792
|
|
|
4793 Checking subalignment 1:
|
|
|
4794 -> OK
|
|
|
4795 Checking subalignment 2:
|
|
|
4796 -> OK
|
|
|
4797 Progressive alignment 2/2...
|
|
|
4798
STEP 21 / 21 (thread 0) f
|
|
|
4799 done.
|
|
|
4800
|
|
|
4801 disttbfast (nuc) Version 7.407
|
|
|
4802 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4803 1 thread(s)
|
|
|
4804
|
|
|
4805 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4806
0 / 22 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4807 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
4808 1 thread(s)
|
|
|
4809
|
|
|
4810 minimumweight = 0.000010
|
|
|
4811 autosubalignment = 0.000000
|
|
|
4812 nthread = 1
|
|
|
4813 randomseed = 0
|
|
|
4814 blosum 62 / kimura 200
|
|
|
4815 poffset = 0
|
|
|
4816 niter = 1
|
|
|
4817 sueff_global = 0.100000
|
|
|
4818 nadd = 1
|
|
|
4819 nsubalignments = 2
|
|
|
4820 maxmem = 16
|
|
|
4821 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4822
|
|
|
4823
|
|
|
4824
0 / 22
10 / 22
20 / 22
|
|
|
4825
|
|
|
4826 Checking subalignment 1:
|
|
|
4827 1 2 3 4 5 6
|
|
|
4828 -> OK
|
|
|
4829
|
|
|
4830 Checking subalignment 2:
|
|
|
4831 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
|
|
|
4832 -> OK
|
|
|
4833 Segment 1/ 1 1- 170
|
|
|
4834 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-1 (thread 1) identical
001-0040-1 (thread 1) worse
|
|
|
4835 Converged.
|
|
|
4836
|
|
|
4837 Reached 1
|
|
|
4838 done
|
|
|
4839 dvtditr (nuc) Version 7.407
|
|
|
4840 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4841 1 thread(s)
|
|
|
4842
|
|
|
4843
|
|
|
4844 Strategy:
|
|
|
4845 FFT-NS-i (Standard)
|
|
|
4846 Iterative refinement method (max. 1 iterations)
|
|
|
4847
|
|
|
4848 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4849 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4850
|
|
|
4851 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4852 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4853 To disable this change, add the --leavegappyregion option.
|
|
|
4854
|
|
|
4855 inputfile = orig
|
|
|
4856 12 x 121 - 96 d
|
|
|
4857 nthread = 1
|
|
|
4858 nthreadpair = 1
|
|
|
4859 nthreadtb = 1
|
|
|
4860 ppenalty_ex = 0
|
|
|
4861 stacksize: 8192 kb
|
|
|
4862 nsubalignments = 2
|
|
|
4863 maxmem = 10
|
|
|
4864 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4865 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4866
|
|
|
4867
|
|
|
4868
|
|
|
4869 Making a distance matrix ..
|
|
|
4870
1 / 12 (thread 0)
|
|
|
4871 done.
|
|
|
4872
|
|
|
4873 Constructing a UPGMA tree ...
|
|
|
4874
|
|
|
4875
0 / 12
|
|
|
4876 ###################################################################
|
|
|
4877 # WARNING: Group 2 is forced to be a monophyletic cluster.
|
|
|
4878 ###################################################################
|
|
|
4879 Reallocated inconsistentpairlist, size=2
|
|
|
4880
10 / 12
|
|
|
4881 done.
|
|
|
4882
|
|
|
4883 Checking subalignment 1:
|
|
|
4884 -> OK
|
|
|
4885 Checking subalignment 2:
|
|
|
4886 -> OK
|
|
|
4887 Progressive alignment 1/2...
|
|
|
4888
STEP 11 / 11 (thread 0) f
|
|
|
4889 done.
|
|
|
4890
|
|
|
4891 Making a distance matrix from msa..
|
|
|
4892
0 / 12 (thread 0)
|
|
|
4893 done.
|
|
|
4894
|
|
|
4895 Constructing a UPGMA tree ...
|
|
|
4896
|
|
|
4897
0 / 12
10 / 12
|
|
|
4898 done.
|
|
|
4899
|
|
|
4900 Checking subalignment 1:
|
|
|
4901 -> OK
|
|
|
4902 Checking subalignment 2:
|
|
|
4903 -> OK
|
|
|
4904 Progressive alignment 2/2...
|
|
|
4905
STEP 11 / 11 (thread 0) f
|
|
|
4906 done.
|
|
|
4907
|
|
|
4908 disttbfast (nuc) Version 7.407
|
|
|
4909 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4910 1 thread(s)
|
|
|
4911
|
|
|
4912 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4913
0 / 12 (thread 0)dndpre (nuc) Version 7.407
|
|
|
4914 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
4915 1 thread(s)
|
|
|
4916
|
|
|
4917 minimumweight = 0.000010
|
|
|
4918 autosubalignment = 0.000000
|
|
|
4919 nthread = 1
|
|
|
4920 randomseed = 0
|
|
|
4921 blosum 62 / kimura 200
|
|
|
4922 poffset = 0
|
|
|
4923 niter = 1
|
|
|
4924 sueff_global = 0.100000
|
|
|
4925 nadd = 1
|
|
|
4926 nsubalignments = 2
|
|
|
4927 maxmem = 10
|
|
|
4928 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4929
|
|
|
4930
|
|
|
4931
0 / 12
10 / 12
|
|
|
4932
|
|
|
4933 Checking subalignment 1:
|
|
|
4934 1 2 3 4 5 6 7 8 9 10
|
|
|
4935 -> OK
|
|
|
4936
|
|
|
4937 Checking subalignment 2:
|
|
|
4938 11 12
|
|
|
4939 -> OK
|
|
|
4940 Segment 1/ 1 1- 122
|
|
|
4941 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-1 (thread 1) identical
001-0020-1 (thread 1) worse
|
|
|
4942 Converged.
|
|
|
4943
|
|
|
4944 Reached 1
|
|
|
4945 done
|
|
|
4946 dvtditr (nuc) Version 7.407
|
|
|
4947 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
4948 1 thread(s)
|
|
|
4949
|
|
|
4950
|
|
|
4951 Strategy:
|
|
|
4952 FFT-NS-i (Standard)
|
|
|
4953 Iterative refinement method (max. 1 iterations)
|
|
|
4954
|
|
|
4955 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
4956 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
4957
|
|
|
4958 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
4959 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
4960 To disable this change, add the --leavegappyregion option.
|
|
|
4961
|
|
|
4962 inputfile = orig
|
|
|
4963 10 x 142 - 88 d
|
|
|
4964 nthread = 1
|
|
|
4965 nthreadpair = 1
|
|
|
4966 nthreadtb = 1
|
|
|
4967 ppenalty_ex = 0
|
|
|
4968 stacksize: 8192 kb
|
|
|
4969 nsubalignments = 2
|
|
|
4970 maxmem = 8
|
|
|
4971 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
4972 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
4973
|
|
|
4974
|
|
|
4975
|
|
|
4976 Making a distance matrix ..
|
|
|
4977
1 / 10 (thread 0)
|
|
|
4978 done.
|
|
|
4979
|
|
|
4980 Constructing a UPGMA tree ...
|
|
|
4981
|
|
|
4982
0 / 10
|
|
|
4983 done.
|
|
|
4984
|
|
|
4985 Checking subalignment 1:
|
|
|
4986 -> OK
|
|
|
4987 Checking subalignment 2:
|
|
|
4988 -> OK
|
|
|
4989 Progressive alignment 1/2...
|
|
|
4990
STEP 9 / 9 (thread 0) f
|
|
|
4991 done.
|
|
|
4992
|
|
|
4993 Making a distance matrix from msa..
|
|
|
4994
0 / 10 (thread 0)
|
|
|
4995 done.
|
|
|
4996
|
|
|
4997 Constructing a UPGMA tree ...
|
|
|
4998
|
|
|
4999
0 / 10
|
|
|
5000 done.
|
|
|
5001
|
|
|
5002 Checking subalignment 1:
|
|
|
5003 -> OK
|
|
|
5004 Checking subalignment 2:
|
|
|
5005 -> OK
|
|
|
5006 Progressive alignment 2/2...
|
|
|
5007
STEP 9 / 9 (thread 0) f
|
|
|
5008 done.
|
|
|
5009
|
|
|
5010 disttbfast (nuc) Version 7.407
|
|
|
5011 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5012 1 thread(s)
|
|
|
5013
|
|
|
5014 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5015
0 / 10 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5016 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5017 1 thread(s)
|
|
|
5018
|
|
|
5019 minimumweight = 0.000010
|
|
|
5020 autosubalignment = 0.000000
|
|
|
5021 nthread = 1
|
|
|
5022 randomseed = 0
|
|
|
5023 blosum 62 / kimura 200
|
|
|
5024 poffset = 0
|
|
|
5025 niter = 1
|
|
|
5026 sueff_global = 0.100000
|
|
|
5027 nadd = 1
|
|
|
5028 nsubalignments = 2
|
|
|
5029 maxmem = 8
|
|
|
5030 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5031
|
|
|
5032
|
|
|
5033
0 / 10
|
|
|
5034
|
|
|
5035 Checking subalignment 1:
|
|
|
5036 1 2
|
|
|
5037 -> OK
|
|
|
5038
|
|
|
5039 Checking subalignment 2:
|
|
|
5040 3 4 5 6 7 8 9 10
|
|
|
5041 -> OK
|
|
|
5042 Segment 1/ 1 1- 157
|
|
|
5043 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-1 (thread 1) identical
001-0016-1 (thread 1) better
|
|
|
5044 Reached 1
|
|
|
5045 done
|
|
|
5046 dvtditr (nuc) Version 7.407
|
|
|
5047 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5048 1 thread(s)
|
|
|
5049
|
|
|
5050
|
|
|
5051 Strategy:
|
|
|
5052 FFT-NS-i (Standard)
|
|
|
5053 Iterative refinement method (max. 1 iterations)
|
|
|
5054
|
|
|
5055 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5056 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5057
|
|
|
5058 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5059 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5060 To disable this change, add the --leavegappyregion option.
|
|
|
5061
|
|
|
5062 inputfile = orig
|
|
|
5063 21 x 168 - 155 d
|
|
|
5064 nthread = 1
|
|
|
5065 nthreadpair = 1
|
|
|
5066 nthreadtb = 1
|
|
|
5067 ppenalty_ex = 0
|
|
|
5068 stacksize: 8192 kb
|
|
|
5069 nsubalignments = 2
|
|
|
5070 maxmem = 17
|
|
|
5071 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5072 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5073
|
|
|
5074
|
|
|
5075
|
|
|
5076 Making a distance matrix ..
|
|
|
5077
1 / 21 (thread 0)
|
|
|
5078 done.
|
|
|
5079
|
|
|
5080 Constructing a UPGMA tree ...
|
|
|
5081
|
|
|
5082
0 / 21
10 / 21
|
|
|
5083 done.
|
|
|
5084
|
|
|
5085 Checking subalignment 1:
|
|
|
5086 -> OK
|
|
|
5087 Checking subalignment 2:
|
|
|
5088 -> OK
|
|
|
5089 Progressive alignment 1/2...
|
|
|
5090
STEP 20 / 20 (thread 0) f
|
|
|
5091 done.
|
|
|
5092
|
|
|
5093 Making a distance matrix from msa..
|
|
|
5094
0 / 21 (thread 0)
|
|
|
5095 done.
|
|
|
5096
|
|
|
5097 Constructing a UPGMA tree ...
|
|
|
5098
|
|
|
5099
0 / 21
10 / 21
|
|
|
5100 done.
|
|
|
5101
|
|
|
5102 Checking subalignment 1:
|
|
|
5103 -> OK
|
|
|
5104 Checking subalignment 2:
|
|
|
5105 -> OK
|
|
|
5106 Progressive alignment 2/2...
|
|
|
5107
STEP 20 / 20 (thread 0) f
|
|
|
5108 done.
|
|
|
5109
|
|
|
5110 disttbfast (nuc) Version 7.407
|
|
|
5111 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5112 1 thread(s)
|
|
|
5113
|
|
|
5114 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5115
0 / 21 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5116 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5117 1 thread(s)
|
|
|
5118
|
|
|
5119 minimumweight = 0.000010
|
|
|
5120 autosubalignment = 0.000000
|
|
|
5121 nthread = 1
|
|
|
5122 randomseed = 0
|
|
|
5123 blosum 62 / kimura 200
|
|
|
5124 poffset = 0
|
|
|
5125 niter = 1
|
|
|
5126 sueff_global = 0.100000
|
|
|
5127 nadd = 1
|
|
|
5128 nsubalignments = 2
|
|
|
5129 maxmem = 17
|
|
|
5130 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5131
|
|
|
5132
|
|
|
5133
0 / 21
10 / 21
|
|
|
5134
|
|
|
5135 Checking subalignment 1:
|
|
|
5136 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
|
|
|
5137 -> OK
|
|
|
5138
|
|
|
5139 Checking subalignment 2:
|
|
|
5140 18 19 20 21
|
|
|
5141 -> OK
|
|
|
5142 Segment 1/ 1 1- 209
|
|
|
5143 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-1 (thread 1) identical
001-0038-1 (thread 1) better
|
|
|
5144 Reached 1
|
|
|
5145 done
|
|
|
5146 dvtditr (nuc) Version 7.407
|
|
|
5147 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5148 1 thread(s)
|
|
|
5149
|
|
|
5150
|
|
|
5151 Strategy:
|
|
|
5152 FFT-NS-i (Standard)
|
|
|
5153 Iterative refinement method (max. 1 iterations)
|
|
|
5154
|
|
|
5155 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5156 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5157
|
|
|
5158 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5159 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5160 To disable this change, add the --leavegappyregion option.
|
|
|
5161
|
|
|
5162 inputfile = orig
|
|
|
5163 12 x 141 - 70 d
|
|
|
5164 nadd = 1
|
|
|
5165 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5166
0 / 11 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5167 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5168 1 thread(s)
|
|
|
5169
|
|
|
5170 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5171 All-to-all alignment.
|
|
|
5172 10 / 11 (by thread 0)
|
|
|
5173
|
|
|
5174 ##### writing hat3
|
|
|
5175 pairlocalalign (nuc) Version 7.407
|
|
|
5176 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5177 1 thread(s)
|
|
|
5178
|
|
|
5179 nadd = 1
|
|
|
5180 ppenalty_ex = -10
|
|
|
5181 nthread = 1
|
|
|
5182 blosum 62 / kimura 200
|
|
|
5183 sueff_global = 0.100000
|
|
|
5184 norg = 11
|
|
|
5185 njobc = 12
|
|
|
5186 Loading 'hat3' ...
|
|
|
5187 done.
|
|
|
5188 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5189 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
5190 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
5191
0 / 1 (thread 0)
c
|
|
|
5192
|
|
|
5193 Combining ..
|
|
|
5194 0 / 1
0 / 1
done.
|
|
|
5195
|
|
|
5196
done.
|
|
|
5197
|
|
|
5198 addsingle (nuc) Version 7.407
|
|
|
5199 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5200 1 thread(s)
|
|
|
5201
|
|
|
5202
|
|
|
5203 Strategy:
|
|
|
5204 Multi-INS-fragment (Not tested.)
|
|
|
5205 ?
|
|
|
5206
|
|
|
5207 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5208 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5209
|
|
|
5210 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5211 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5212 To disable this change, add the --leavegappyregion option.
|
|
|
5213
|
|
|
5214 inputfile = orig
|
|
|
5215 24 x 169 - 74 d
|
|
|
5216 nthread = 1
|
|
|
5217 nthreadpair = 1
|
|
|
5218 nthreadtb = 1
|
|
|
5219 ppenalty_ex = 0
|
|
|
5220 stacksize: 8192 kb
|
|
|
5221 nsubalignments = 2
|
|
|
5222 maxmem = 22
|
|
|
5223 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5224 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5225
|
|
|
5226
|
|
|
5227
|
|
|
5228 Making a distance matrix ..
|
|
|
5229
1 / 24 (thread 0)
|
|
|
5230 done.
|
|
|
5231
|
|
|
5232 Constructing a UPGMA tree ...
|
|
|
5233
|
|
|
5234
0 / 24
10 / 24
20 / 24
|
|
|
5235 done.
|
|
|
5236
|
|
|
5237 Checking subalignment 1:
|
|
|
5238 -> OK
|
|
|
5239 Checking subalignment 2:
|
|
|
5240 -> OK
|
|
|
5241 Progressive alignment 1/2...
|
|
|
5242
STEP 23 / 23 (thread 0) f
|
|
|
5243 done.
|
|
|
5244
|
|
|
5245 Making a distance matrix from msa..
|
|
|
5246
0 / 24 (thread 0)
|
|
|
5247 done.
|
|
|
5248
|
|
|
5249 Constructing a UPGMA tree ...
|
|
|
5250
|
|
|
5251
0 / 24
10 / 24
20 / 24
|
|
|
5252 done.
|
|
|
5253
|
|
|
5254 Checking subalignment 1:
|
|
|
5255 -> OK
|
|
|
5256 Checking subalignment 2:
|
|
|
5257 -> OK
|
|
|
5258 Progressive alignment 2/2...
|
|
|
5259
STEP 23 / 23 (thread 0) f
|
|
|
5260 done.
|
|
|
5261
|
|
|
5262 disttbfast (nuc) Version 7.407
|
|
|
5263 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5264 1 thread(s)
|
|
|
5265
|
|
|
5266 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5267
0 / 24 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5268 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5269 1 thread(s)
|
|
|
5270
|
|
|
5271 minimumweight = 0.000010
|
|
|
5272 autosubalignment = 0.000000
|
|
|
5273 nthread = 1
|
|
|
5274 randomseed = 0
|
|
|
5275 blosum 62 / kimura 200
|
|
|
5276 poffset = 0
|
|
|
5277 niter = 1
|
|
|
5278 sueff_global = 0.100000
|
|
|
5279 nadd = 1
|
|
|
5280 nsubalignments = 2
|
|
|
5281 maxmem = 22
|
|
|
5282 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5283
|
|
|
5284
|
|
|
5285
0 / 24
10 / 24
20 / 24
|
|
|
5286
|
|
|
5287 Checking subalignment 1:
|
|
|
5288 1 2
|
|
|
5289 -> OK
|
|
|
5290
|
|
|
5291 Checking subalignment 2:
|
|
|
5292 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
|
|
|
5293 -> OK
|
|
|
5294 Segment 1/ 1 1- 174
|
|
|
5295 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-0 (thread 1) skip
001-0043-1 (thread 1) skip
001-0044-1 (thread 1) identical
001-0044-1 (thread 1) better
|
|
|
5296 Reached 1
|
|
|
5297 done
|
|
|
5298 dvtditr (nuc) Version 7.407
|
|
|
5299 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5300 1 thread(s)
|
|
|
5301
|
|
|
5302
|
|
|
5303 Strategy:
|
|
|
5304 FFT-NS-i (Standard)
|
|
|
5305 Iterative refinement method (max. 1 iterations)
|
|
|
5306
|
|
|
5307 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5308 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5309
|
|
|
5310 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5311 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5312 To disable this change, add the --leavegappyregion option.
|
|
|
5313
|
|
|
5314 inputfile = orig
|
|
|
5315 13 x 121 - 70 d
|
|
|
5316 nadd = 1
|
|
|
5317 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5318
0 / 12 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5319 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5320 1 thread(s)
|
|
|
5321
|
|
|
5322 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5323 All-to-all alignment.
|
|
|
5324
|
|
|
5325
|
|
|
5326 ##### writing hat3
|
|
|
5327 pairlocalalign (nuc) Version 7.407
|
|
|
5328 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5329 1 thread(s)
|
|
|
5330
|
|
|
5331 nadd = 1
|
|
|
5332 ppenalty_ex = -10
|
|
|
5333 nthread = 1
|
|
|
5334 blosum 62 / kimura 200
|
|
|
5335 sueff_global = 0.100000
|
|
|
5336 norg = 12
|
|
|
5337 njobc = 13
|
|
|
5338 Loading 'hat3' ...
|
|
|
5339 done.
|
|
|
5340 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5341 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
5342 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
5343
0 / 1 (thread 0)
c
|
|
|
5344
|
|
|
5345 Combining ..
|
|
|
5346 0 / 1
0 / 1
done.
|
|
|
5347
|
|
|
5348
done.
|
|
|
5349
|
|
|
5350 addsingle (nuc) Version 7.407
|
|
|
5351 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5352 1 thread(s)
|
|
|
5353
|
|
|
5354
|
|
|
5355 Strategy:
|
|
|
5356 Multi-INS-fragment (Not tested.)
|
|
|
5357 ?
|
|
|
5358
|
|
|
5359 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5360 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5361
|
|
|
5362 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5363 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5364 To disable this change, add the --leavegappyregion option.
|
|
|
5365
|
|
|
5366 inputfile = orig
|
|
|
5367 26 x 186 - 107 d
|
|
|
5368 nthread = 1
|
|
|
5369 nthreadpair = 1
|
|
|
5370 nthreadtb = 1
|
|
|
5371 ppenalty_ex = 0
|
|
|
5372 stacksize: 8192 kb
|
|
|
5373 nsubalignments = 2
|
|
|
5374 maxmem = 21
|
|
|
5375 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5376 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5377
|
|
|
5378
|
|
|
5379
|
|
|
5380 Making a distance matrix ..
|
|
|
5381
1 / 26 (thread 0)
|
|
|
5382 done.
|
|
|
5383
|
|
|
5384 Constructing a UPGMA tree ...
|
|
|
5385
|
|
|
5386
0 / 26
10 / 26
20 / 26
|
|
|
5387 done.
|
|
|
5388
|
|
|
5389 Checking subalignment 1:
|
|
|
5390 -> OK
|
|
|
5391 Checking subalignment 2:
|
|
|
5392 -> OK
|
|
|
5393 Progressive alignment 1/2...
|
|
|
5394
STEP 25 / 25 (thread 0) f
|
|
|
5395 done.
|
|
|
5396
|
|
|
5397 Making a distance matrix from msa..
|
|
|
5398
0 / 26 (thread 0)
|
|
|
5399 done.
|
|
|
5400
|
|
|
5401 Constructing a UPGMA tree ...
|
|
|
5402
|
|
|
5403
0 / 26
10 / 26
20 / 26
|
|
|
5404 done.
|
|
|
5405
|
|
|
5406 Checking subalignment 1:
|
|
|
5407 -> OK
|
|
|
5408 Checking subalignment 2:
|
|
|
5409 -> OK
|
|
|
5410 Progressive alignment 2/2...
|
|
|
5411
STEP 25 / 25 (thread 0) f
|
|
|
5412 done.
|
|
|
5413
|
|
|
5414 disttbfast (nuc) Version 7.407
|
|
|
5415 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5416 1 thread(s)
|
|
|
5417
|
|
|
5418 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5419
0 / 26 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5420 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5421 1 thread(s)
|
|
|
5422
|
|
|
5423 minimumweight = 0.000010
|
|
|
5424 autosubalignment = 0.000000
|
|
|
5425 nthread = 1
|
|
|
5426 randomseed = 0
|
|
|
5427 blosum 62 / kimura 200
|
|
|
5428 poffset = 0
|
|
|
5429 niter = 1
|
|
|
5430 sueff_global = 0.100000
|
|
|
5431 nadd = 1
|
|
|
5432 nsubalignments = 2
|
|
|
5433 maxmem = 21
|
|
|
5434 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5435
|
|
|
5436
|
|
|
5437
0 / 26
10 / 26
20 / 26
|
|
|
5438
|
|
|
5439 Checking subalignment 1:
|
|
|
5440 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
|
|
|
5441 -> OK
|
|
|
5442
|
|
|
5443 Checking subalignment 2:
|
|
|
5444 22 23 24 25 26
|
|
|
5445 -> OK
|
|
|
5446 Segment 1/ 1 1- 199
|
|
|
5447 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-0 (thread 1) skip
001-0043-1 (thread 1) skip
001-0044-0 (thread 1) skip
001-0045-1 (thread 1) skip
001-0046-0 (thread 1) skip
001-0047-1 (thread 1) skip
001-0048-1 (thread 1) identical
001-0048-1 (thread 1) worse
|
|
|
5448 Converged.
|
|
|
5449
|
|
|
5450 Reached 1
|
|
|
5451 done
|
|
|
5452 dvtditr (nuc) Version 7.407
|
|
|
5453 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5454 1 thread(s)
|
|
|
5455
|
|
|
5456
|
|
|
5457 Strategy:
|
|
|
5458 FFT-NS-i (Standard)
|
|
|
5459 Iterative refinement method (max. 1 iterations)
|
|
|
5460
|
|
|
5461 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5462 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5463
|
|
|
5464 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5465 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5466 To disable this change, add the --leavegappyregion option.
|
|
|
5467
|
|
|
5468 inputfile = orig
|
|
|
5469 25 x 173 - 70 d
|
|
|
5470 nadd = 1
|
|
|
5471 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5472
0 / 24 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5473 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5474 1 thread(s)
|
|
|
5475
|
|
|
5476 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5477 All-to-all alignment.
|
|
|
5478
|
|
|
5479
|
|
|
5480 ##### writing hat3
|
|
|
5481 pairlocalalign (nuc) Version 7.407
|
|
|
5482 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5483 1 thread(s)
|
|
|
5484
|
|
|
5485 nadd = 1
|
|
|
5486 ppenalty_ex = -10
|
|
|
5487 nthread = 1
|
|
|
5488 blosum 62 / kimura 200
|
|
|
5489 sueff_global = 0.100000
|
|
|
5490 norg = 24
|
|
|
5491 njobc = 25
|
|
|
5492 Loading 'hat3' ...
|
|
|
5493 done.
|
|
|
5494 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5495 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
5496 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
5497
0 / 1 (thread 0)
c
|
|
|
5498
|
|
|
5499 Combining ..
|
|
|
5500 0 / 1
0 / 1
done.
|
|
|
5501
|
|
|
5502
done.
|
|
|
5503
|
|
|
5504 addsingle (nuc) Version 7.407
|
|
|
5505 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5506 1 thread(s)
|
|
|
5507
|
|
|
5508
|
|
|
5509 Strategy:
|
|
|
5510 Multi-INS-fragment (Not tested.)
|
|
|
5511 ?
|
|
|
5512
|
|
|
5513 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5514 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5515
|
|
|
5516 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5517 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5518 To disable this change, add the --leavegappyregion option.
|
|
|
5519
|
|
|
5520 inputfile = orig
|
|
|
5521 23 x 142 - 130 d
|
|
|
5522 nthread = 1
|
|
|
5523 nthreadpair = 1
|
|
|
5524 nthreadtb = 1
|
|
|
5525 ppenalty_ex = 0
|
|
|
5526 stacksize: 8192 kb
|
|
|
5527 nsubalignments = 2
|
|
|
5528 maxmem = 13
|
|
|
5529 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5530 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5531
|
|
|
5532
|
|
|
5533
|
|
|
5534 Making a distance matrix ..
|
|
|
5535
1 / 23 (thread 0)
|
|
|
5536 done.
|
|
|
5537
|
|
|
5538 Constructing a UPGMA tree ...
|
|
|
5539
|
|
|
5540
0 / 23
10 / 23
20 / 23
|
|
|
5541 done.
|
|
|
5542
|
|
|
5543 Checking subalignment 1:
|
|
|
5544 -> OK
|
|
|
5545 Checking subalignment 2:
|
|
|
5546 -> OK
|
|
|
5547 Progressive alignment 1/2...
|
|
|
5548
STEP 22 / 22 (thread 0) f
|
|
|
5549 done.
|
|
|
5550
|
|
|
5551 Making a distance matrix from msa..
|
|
|
5552
0 / 23 (thread 0)
|
|
|
5553 done.
|
|
|
5554
|
|
|
5555 Constructing a UPGMA tree ...
|
|
|
5556
|
|
|
5557
0 / 23
10 / 23
20 / 23
|
|
|
5558 done.
|
|
|
5559
|
|
|
5560 Checking subalignment 1:
|
|
|
5561 -> OK
|
|
|
5562 Checking subalignment 2:
|
|
|
5563 -> OK
|
|
|
5564 Progressive alignment 2/2...
|
|
|
5565
STEP 22 / 22 (thread 0) f
|
|
|
5566 done.
|
|
|
5567
|
|
|
5568 disttbfast (nuc) Version 7.407
|
|
|
5569 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5570 1 thread(s)
|
|
|
5571
|
|
|
5572 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5573
0 / 23 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5574 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5575 1 thread(s)
|
|
|
5576
|
|
|
5577 minimumweight = 0.000010
|
|
|
5578 autosubalignment = 0.000000
|
|
|
5579 nthread = 1
|
|
|
5580 randomseed = 0
|
|
|
5581 blosum 62 / kimura 200
|
|
|
5582 poffset = 0
|
|
|
5583 niter = 1
|
|
|
5584 sueff_global = 0.100000
|
|
|
5585 nadd = 1
|
|
|
5586 nsubalignments = 2
|
|
|
5587 maxmem = 13
|
|
|
5588 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5589
|
|
|
5590
|
|
|
5591
0 / 23
10 / 23
20 / 23
|
|
|
5592
|
|
|
5593 Checking subalignment 1:
|
|
|
5594 1 2 3 4 5 6 7 8 9 10 11 12 13
|
|
|
5595 -> OK
|
|
|
5596
|
|
|
5597 Checking subalignment 2:
|
|
|
5598 14 15 16 17 18 19 20 21 22 23
|
|
|
5599 -> OK
|
|
|
5600 Segment 1/ 1 1- 155
|
|
|
5601 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-1 (thread 1) identical
|
|
|
5602 Converged.
|
|
|
5603
|
|
|
5604 Reached 1
|
|
|
5605 done
|
|
|
5606 dvtditr (nuc) Version 7.407
|
|
|
5607 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5608 1 thread(s)
|
|
|
5609
|
|
|
5610
|
|
|
5611 Strategy:
|
|
|
5612 FFT-NS-i (Standard)
|
|
|
5613 Iterative refinement method (max. 1 iterations)
|
|
|
5614
|
|
|
5615 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5616 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5617
|
|
|
5618 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5619 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5620 To disable this change, add the --leavegappyregion option.
|
|
|
5621
|
|
|
5622 inputfile = orig
|
|
|
5623 38 x 198 - 155 d
|
|
|
5624 nthread = 1
|
|
|
5625 nthreadpair = 1
|
|
|
5626 nthreadtb = 1
|
|
|
5627 ppenalty_ex = 0
|
|
|
5628 stacksize: 8192 kb
|
|
|
5629 nsubalignments = 2
|
|
|
5630 maxmem = 26
|
|
|
5631 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5632 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5633
|
|
|
5634
|
|
|
5635
|
|
|
5636 Making a distance matrix ..
|
|
|
5637
1 / 38 (thread 0)
|
|
|
5638 done.
|
|
|
5639
|
|
|
5640 Constructing a UPGMA tree ...
|
|
|
5641
|
|
|
5642
0 / 38
10 / 38
20 / 38
30 / 38
|
|
|
5643 done.
|
|
|
5644
|
|
|
5645 Checking subalignment 1:
|
|
|
5646 -> OK
|
|
|
5647 Checking subalignment 2:
|
|
|
5648 -> OK
|
|
|
5649 Progressive alignment 1/2...
|
|
|
5650
STEP 37 / 37 (thread 0) f
|
|
|
5651 done.
|
|
|
5652
|
|
|
5653 Making a distance matrix from msa..
|
|
|
5654
0 / 38 (thread 0)
|
|
|
5655 done.
|
|
|
5656
|
|
|
5657 Constructing a UPGMA tree ...
|
|
|
5658
|
|
|
5659
0 / 38
10 / 38
20 / 38
30 / 38
|
|
|
5660 done.
|
|
|
5661
|
|
|
5662 Checking subalignment 1:
|
|
|
5663 -> OK
|
|
|
5664 Checking subalignment 2:
|
|
|
5665 -> OK
|
|
|
5666 Progressive alignment 2/2...
|
|
|
5667
STEP 37 / 37 (thread 0) f
|
|
|
5668 done.
|
|
|
5669
|
|
|
5670 disttbfast (nuc) Version 7.407
|
|
|
5671 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5672 1 thread(s)
|
|
|
5673
|
|
|
5674 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5675
0 / 38 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5676 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5677 1 thread(s)
|
|
|
5678
|
|
|
5679 minimumweight = 0.000010
|
|
|
5680 autosubalignment = 0.000000
|
|
|
5681 nthread = 1
|
|
|
5682 randomseed = 0
|
|
|
5683 blosum 62 / kimura 200
|
|
|
5684 poffset = 0
|
|
|
5685 niter = 1
|
|
|
5686 sueff_global = 0.100000
|
|
|
5687 nadd = 1
|
|
|
5688 nsubalignments = 2
|
|
|
5689 maxmem = 26
|
|
|
5690 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5691
|
|
|
5692
|
|
|
5693
0 / 38
10 / 38
20 / 38
30 / 38
|
|
|
5694
|
|
|
5695 Checking subalignment 1:
|
|
|
5696 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
|
|
|
5697 -> OK
|
|
|
5698
|
|
|
5699 Checking subalignment 2:
|
|
|
5700 27 28 29 30 31 32 33 34 35 36 37 38
|
|
|
5701 -> OK
|
|
|
5702 Segment 1/ 1 1- 205
|
|
|
5703 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-0 (thread 1) skip
001-0043-1 (thread 1) skip
001-0044-0 (thread 1) skip
001-0045-1 (thread 1) skip
001-0046-0 (thread 1) skip
001-0047-1 (thread 1) skip
001-0048-0 (thread 1) skip
001-0049-1 (thread 1) skip
001-0050-0 (thread 1) skip
001-0051-1 (thread 1) skip
001-0052-0 (thread 1) skip
001-0053-1 (thread 1) skip
001-0054-0 (thread 1) skip
001-0055-1 (thread 1) skip
001-0056-0 (thread 1) skip
001-0057-1 (thread 1) skip
001-0058-0 (thread 1) skip
001-0059-1 (thread 1) skip
001-0060-0 (thread 1) skip
001-0061-1 (thread 1) skip
001-0062-0 (thread 1) skip
001-0063-1 (thread 1) skip
001-0064-0 (thread 1) skip
001-0065-1 (thread 1) skip
001-0066-0 (thread 1) skip
001-0067-1 (thread 1) skip
001-0068-0 (thread 1) skip
001-0069-1 (thread 1) skip
001-0070-0 (thread 1) skip
001-0071-1 (thread 1) skip
001-0072-1 (thread 1) identical
001-0072-1 (thread 1) better
|
|
|
5704 Reached 1
|
|
|
5705 done
|
|
|
5706 dvtditr (nuc) Version 7.407
|
|
|
5707 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5708 1 thread(s)
|
|
|
5709
|
|
|
5710
|
|
|
5711 Strategy:
|
|
|
5712 FFT-NS-i (Standard)
|
|
|
5713 Iterative refinement method (max. 1 iterations)
|
|
|
5714
|
|
|
5715 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5716 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5717
|
|
|
5718 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5719 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5720 To disable this change, add the --leavegappyregion option.
|
|
|
5721
|
|
|
5722 inputfile = orig
|
|
|
5723 34 x 182 - 104 d
|
|
|
5724 nthread = 1
|
|
|
5725 nthreadpair = 1
|
|
|
5726 nthreadtb = 1
|
|
|
5727 ppenalty_ex = 0
|
|
|
5728 stacksize: 8192 kb
|
|
|
5729 nsubalignments = 2
|
|
|
5730 maxmem = 25
|
|
|
5731 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5732 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5733
|
|
|
5734
|
|
|
5735
|
|
|
5736 Making a distance matrix ..
|
|
|
5737
1 / 34 (thread 0)
|
|
|
5738 done.
|
|
|
5739
|
|
|
5740 Constructing a UPGMA tree ...
|
|
|
5741
|
|
|
5742
0 / 34
10 / 34
20 / 34
30 / 34
|
|
|
5743 done.
|
|
|
5744
|
|
|
5745 Checking subalignment 1:
|
|
|
5746 -> OK
|
|
|
5747 Checking subalignment 2:
|
|
|
5748 -> OK
|
|
|
5749 Progressive alignment 1/2...
|
|
|
5750
STEP 33 / 33 (thread 0) f
|
|
|
5751 done.
|
|
|
5752
|
|
|
5753 Making a distance matrix from msa..
|
|
|
5754
0 / 34 (thread 0)
|
|
|
5755 done.
|
|
|
5756
|
|
|
5757 Constructing a UPGMA tree ...
|
|
|
5758
|
|
|
5759
0 / 34
10 / 34
20 / 34
30 / 34
|
|
|
5760 done.
|
|
|
5761
|
|
|
5762 Checking subalignment 1:
|
|
|
5763 -> OK
|
|
|
5764 Checking subalignment 2:
|
|
|
5765 -> OK
|
|
|
5766 Progressive alignment 2/2...
|
|
|
5767
STEP 33 / 33 (thread 0) f
|
|
|
5768 done.
|
|
|
5769
|
|
|
5770 disttbfast (nuc) Version 7.407
|
|
|
5771 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5772 1 thread(s)
|
|
|
5773
|
|
|
5774 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5775
0 / 34 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5776 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5777 1 thread(s)
|
|
|
5778
|
|
|
5779 minimumweight = 0.000010
|
|
|
5780 autosubalignment = 0.000000
|
|
|
5781 nthread = 1
|
|
|
5782 randomseed = 0
|
|
|
5783 blosum 62 / kimura 200
|
|
|
5784 poffset = 0
|
|
|
5785 niter = 1
|
|
|
5786 sueff_global = 0.100000
|
|
|
5787 nadd = 1
|
|
|
5788 nsubalignments = 2
|
|
|
5789 maxmem = 25
|
|
|
5790 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5791
|
|
|
5792
|
|
|
5793
0 / 34
10 / 34
20 / 34
30 / 34
|
|
|
5794
|
|
|
5795 Checking subalignment 1:
|
|
|
5796 1 2 3 4 5 6 7 8 9
|
|
|
5797 -> OK
|
|
|
5798
|
|
|
5799 Checking subalignment 2:
|
|
|
5800 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
|
|
|
5801 -> OK
|
|
|
5802 Segment 1/ 1 1- 188
|
|
|
5803 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-0 (thread 1) skip
001-0043-1 (thread 1) skip
001-0044-0 (thread 1) skip
001-0045-1 (thread 1) skip
001-0046-0 (thread 1) skip
001-0047-1 (thread 1) skip
001-0048-0 (thread 1) skip
001-0049-1 (thread 1) skip
001-0050-0 (thread 1) skip
001-0051-1 (thread 1) skip
001-0052-0 (thread 1) skip
001-0053-1 (thread 1) skip
001-0054-0 (thread 1) skip
001-0055-1 (thread 1) skip
001-0056-0 (thread 1) skip
001-0057-1 (thread 1) skip
001-0058-0 (thread 1) skip
001-0059-1 (thread 1) skip
001-0060-0 (thread 1) skip
001-0061-1 (thread 1) skip
001-0062-0 (thread 1) skip
001-0063-1 (thread 1) skip
001-0064-1 (thread 1) identical
001-0064-1 (thread 1) better
|
|
|
5804 Reached 1
|
|
|
5805 done
|
|
|
5806 dvtditr (nuc) Version 7.407
|
|
|
5807 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5808 1 thread(s)
|
|
|
5809
|
|
|
5810
|
|
|
5811 Strategy:
|
|
|
5812 FFT-NS-i (Standard)
|
|
|
5813 Iterative refinement method (max. 1 iterations)
|
|
|
5814
|
|
|
5815 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5816 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5817
|
|
|
5818 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5819 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5820 To disable this change, add the --leavegappyregion option.
|
|
|
5821
|
|
|
5822 inputfile = orig
|
|
|
5823 24 x 154 - 70 d
|
|
|
5824 nadd = 1
|
|
|
5825 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5826
0 / 23 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5827 alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5828 1 thread(s)
|
|
|
5829
|
|
|
5830 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5831 All-to-all alignment.
|
|
|
5832
|
|
|
5833
|
|
|
5834 ##### writing hat3
|
|
|
5835 pairlocalalign (nuc) Version 7.407
|
|
|
5836 alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
|
|
|
5837 1 thread(s)
|
|
|
5838
|
|
|
5839 nadd = 1
|
|
|
5840 ppenalty_ex = -10
|
|
|
5841 nthread = 1
|
|
|
5842 blosum 62 / kimura 200
|
|
|
5843 sueff_global = 0.100000
|
|
|
5844 norg = 23
|
|
|
5845 njobc = 24
|
|
|
5846 Loading 'hat3' ...
|
|
|
5847 done.
|
|
|
5848 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5849 Loading 'hat2n' (aligned sequences - new sequences) ... done.
|
|
|
5850 Loading 'hat2i' (aligned sequences) ... done.
|
|
|
5851
0 / 1 (thread 0)
c
|
|
|
5852
|
|
|
5853 Combining ..
|
|
|
5854 0 / 1
0 / 1
done.
|
|
|
5855
|
|
|
5856
done.
|
|
|
5857
|
|
|
5858 addsingle (nuc) Version 7.407
|
|
|
5859 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5860 1 thread(s)
|
|
|
5861
|
|
|
5862
|
|
|
5863 Strategy:
|
|
|
5864 Multi-INS-fragment (Not tested.)
|
|
|
5865 ?
|
|
|
5866
|
|
|
5867 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5868 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5869
|
|
|
5870 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5871 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5872 To disable this change, add the --leavegappyregion option.
|
|
|
5873
|
|
|
5874 inputfile = orig
|
|
|
5875 38 x 187 - 149 d
|
|
|
5876 nthread = 1
|
|
|
5877 nthreadpair = 1
|
|
|
5878 nthreadtb = 1
|
|
|
5879 ppenalty_ex = 0
|
|
|
5880 stacksize: 8192 kb
|
|
|
5881 nsubalignments = 2
|
|
|
5882 maxmem = 34
|
|
|
5883 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5884 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5885
|
|
|
5886
|
|
|
5887
|
|
|
5888 Making a distance matrix ..
|
|
|
5889
1 / 38 (thread 0)
|
|
|
5890 done.
|
|
|
5891
|
|
|
5892 Constructing a UPGMA tree ...
|
|
|
5893
|
|
|
5894
0 / 38
10 / 38
20 / 38
30 / 38
|
|
|
5895 done.
|
|
|
5896
|
|
|
5897 Checking subalignment 1:
|
|
|
5898 -> OK
|
|
|
5899 Checking subalignment 2:
|
|
|
5900 -> OK
|
|
|
5901 Progressive alignment 1/2...
|
|
|
5902
STEP 37 / 37 (thread 0) f
|
|
|
5903 done.
|
|
|
5904
|
|
|
5905 Making a distance matrix from msa..
|
|
|
5906
0 / 38 (thread 0)
|
|
|
5907 done.
|
|
|
5908
|
|
|
5909 Constructing a UPGMA tree ...
|
|
|
5910
|
|
|
5911
0 / 38
10 / 38
20 / 38
30 / 38
|
|
|
5912 done.
|
|
|
5913
|
|
|
5914 Checking subalignment 1:
|
|
|
5915 -> OK
|
|
|
5916 Checking subalignment 2:
|
|
|
5917 -> OK
|
|
|
5918 Progressive alignment 2/2...
|
|
|
5919
STEP 37 / 37 (thread 0) f
|
|
|
5920 done.
|
|
|
5921
|
|
|
5922 disttbfast (nuc) Version 7.407
|
|
|
5923 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5924 1 thread(s)
|
|
|
5925
|
|
|
5926 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5927
0 / 38 (thread 0)dndpre (nuc) Version 7.407
|
|
|
5928 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
5929 1 thread(s)
|
|
|
5930
|
|
|
5931 minimumweight = 0.000010
|
|
|
5932 autosubalignment = 0.000000
|
|
|
5933 nthread = 1
|
|
|
5934 randomseed = 0
|
|
|
5935 blosum 62 / kimura 200
|
|
|
5936 poffset = 0
|
|
|
5937 niter = 1
|
|
|
5938 sueff_global = 0.100000
|
|
|
5939 nadd = 1
|
|
|
5940 nsubalignments = 2
|
|
|
5941 maxmem = 34
|
|
|
5942 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5943
|
|
|
5944
|
|
|
5945
0 / 38
10 / 38
20 / 38
30 / 38
|
|
|
5946
|
|
|
5947 Checking subalignment 1:
|
|
|
5948 1 2 3 4
|
|
|
5949 -> OK
|
|
|
5950
|
|
|
5951 Checking subalignment 2:
|
|
|
5952 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
|
|
|
5953 -> OK
|
|
|
5954 Segment 1/ 1 1- 216
|
|
|
5955 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-0 (thread 1) skip
001-0043-1 (thread 1) skip
001-0044-0 (thread 1) skip
001-0045-1 (thread 1) skip
001-0046-0 (thread 1) skip
001-0047-1 (thread 1) skip
001-0048-0 (thread 1) skip
001-0049-1 (thread 1) skip
001-0050-0 (thread 1) skip
001-0051-1 (thread 1) skip
001-0052-0 (thread 1) skip
001-0053-1 (thread 1) skip
001-0054-0 (thread 1) skip
001-0055-1 (thread 1) skip
001-0056-0 (thread 1) skip
001-0057-1 (thread 1) skip
001-0058-0 (thread 1) skip
001-0059-1 (thread 1) skip
001-0060-0 (thread 1) skip
001-0061-1 (thread 1) skip
001-0062-0 (thread 1) skip
001-0063-1 (thread 1) skip
001-0064-0 (thread 1) skip
001-0065-1 (thread 1) skip
001-0066-0 (thread 1) skip
001-0067-1 (thread 1) skip
001-0068-0 (thread 1) skip
001-0069-1 (thread 1) skip
001-0070-0 (thread 1) skip
001-0071-1 (thread 1) skip
001-0072-1 (thread 1) identical
001-0072-1 (thread 1) worse
|
|
|
5956 Converged.
|
|
|
5957
|
|
|
5958 Reached 1
|
|
|
5959 done
|
|
|
5960 dvtditr (nuc) Version 7.407
|
|
|
5961 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
5962 1 thread(s)
|
|
|
5963
|
|
|
5964
|
|
|
5965 Strategy:
|
|
|
5966 FFT-NS-i (Standard)
|
|
|
5967 Iterative refinement method (max. 1 iterations)
|
|
|
5968
|
|
|
5969 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
5970 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
5971
|
|
|
5972 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
5973 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
5974 To disable this change, add the --leavegappyregion option.
|
|
|
5975
|
|
|
5976 inputfile = orig
|
|
|
5977 76 x 215 - 206 d
|
|
|
5978 nthread = 1
|
|
|
5979 nthreadpair = 1
|
|
|
5980 nthreadtb = 1
|
|
|
5981 ppenalty_ex = 0
|
|
|
5982 stacksize: 8192 kb
|
|
|
5983 nsubalignments = 2
|
|
|
5984 maxmem = 38
|
|
|
5985 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
5986 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
5987
|
|
|
5988
|
|
|
5989
|
|
|
5990 Making a distance matrix ..
|
|
|
5991
1 / 76 (thread 0)
|
|
|
5992 done.
|
|
|
5993
|
|
|
5994 Constructing a UPGMA tree ...
|
|
|
5995
|
|
|
5996
0 / 76
10 / 76
20 / 76
30 / 76
40 / 76
50 / 76
60 / 76
70 / 76
|
|
|
5997 done.
|
|
|
5998
|
|
|
5999 Checking subalignment 1:
|
|
|
6000 -> OK
|
|
|
6001 Checking subalignment 2:
|
|
|
6002 -> OK
|
|
|
6003 Progressive alignment 1/2...
|
|
|
6004
STEP 75 / 75 (thread 0) f
|
|
|
6005 done.
|
|
|
6006
|
|
|
6007 Making a distance matrix from msa..
|
|
|
6008
0 / 76 (thread 0)
|
|
|
6009 done.
|
|
|
6010
|
|
|
6011 Constructing a UPGMA tree ...
|
|
|
6012
|
|
|
6013
0 / 76
10 / 76
20 / 76
30 / 76
40 / 76
50 / 76
60 / 76
70 / 76
|
|
|
6014 done.
|
|
|
6015
|
|
|
6016 Checking subalignment 1:
|
|
|
6017 -> OK
|
|
|
6018 Checking subalignment 2:
|
|
|
6019 -> OK
|
|
|
6020 Progressive alignment 2/2...
|
|
|
6021
STEP 75 / 75 (thread 0) f
|
|
|
6022 done.
|
|
|
6023
|
|
|
6024 disttbfast (nuc) Version 7.407
|
|
|
6025 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
6026 1 thread(s)
|
|
|
6027
|
|
|
6028 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
6029
0 / 76 (thread 0)dndpre (nuc) Version 7.407
|
|
|
6030 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
6031 1 thread(s)
|
|
|
6032
|
|
|
6033 minimumweight = 0.000010
|
|
|
6034 autosubalignment = 0.000000
|
|
|
6035 nthread = 1
|
|
|
6036 randomseed = 0
|
|
|
6037 blosum 62 / kimura 200
|
|
|
6038 poffset = 0
|
|
|
6039 niter = 1
|
|
|
6040 sueff_global = 0.100000
|
|
|
6041 nadd = 1
|
|
|
6042 nsubalignments = 2
|
|
|
6043 maxmem = 38
|
|
|
6044 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
6045
|
|
|
6046
|
|
|
6047
0 / 76
10 / 76
20 / 76
30 / 76
40 / 76
50 / 76
60 / 76
70 / 76
|
|
|
6048
|
|
|
6049 Checking subalignment 1:
|
|
|
6050 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
|
|
|
6051 -> OK
|
|
|
6052
|
|
|
6053 Checking subalignment 2:
|
|
|
6054 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76
|
|
|
6055 -> OK
|
|
|
6056 Segment 1/ 1 1- 285
|
|
|
6057 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-0 (thread 1) skip
001-0043-1 (thread 1) skip
001-0044-0 (thread 1) skip
001-0045-1 (thread 1) skip
001-0046-0 (thread 1) skip
001-0047-1 (thread 1) skip
001-0048-0 (thread 1) skip
001-0049-1 (thread 1) skip
001-0050-0 (thread 1) skip
001-0051-1 (thread 1) skip
001-0052-0 (thread 1) skip
001-0053-1 (thread 1) skip
001-0054-0 (thread 1) skip
001-0055-1 (thread 1) skip
001-0056-0 (thread 1) skip
001-0057-1 (thread 1) skip
001-0058-0 (thread 1) skip
001-0059-1 (thread 1) skip
001-0060-0 (thread 1) skip
001-0061-1 (thread 1) skip
001-0062-0 (thread 1) skip
001-0063-1 (thread 1) skip
001-0064-0 (thread 1) skip
001-0065-1 (thread 1) skip
001-0066-0 (thread 1) skip
001-0067-1 (thread 1) skip
001-0068-0 (thread 1) skip
001-0069-1 (thread 1) skip
001-0070-0 (thread 1) skip
001-0071-1 (thread 1) skip
001-0072-0 (thread 1) skip
001-0073-1 (thread 1) skip
001-0074-0 (thread 1) skip
001-0075-1 (thread 1) skip
001-0076-0 (thread 1) skip
001-0077-1 (thread 1) skip
001-0078-0 (thread 1) skip
001-0079-1 (thread 1) skip
001-0080-0 (thread 1) skip
001-0081-1 (thread 1) skip
001-0082-0 (thread 1) skip
001-0083-1 (thread 1) skip
001-0084-0 (thread 1) skip
001-0085-1 (thread 1) skip
001-0086-0 (thread 1) skip
001-0087-1 (thread 1) skip
001-0088-0 (thread 1) skip
001-0089-1 (thread 1) skip
001-0090-0 (thread 1) skip
001-0091-1 (thread 1) skip
001-0092-0 (thread 1) skip
001-0093-1 (thread 1) skip
001-0094-0 (thread 1) skip
001-0095-1 (thread 1) skip
001-0096-0 (thread 1) skip
001-0097-1 (thread 1) skip
001-0098-0 (thread 1) skip
001-0099-1 (thread 1) skip
001-0100-0 (thread 1) skip
001-0101-1 (thread 1) skip
001-0102-0 (thread 1) skip
001-0103-1 (thread 1) skip
001-0104-0 (thread 1) skip
001-0105-1 (thread 1) skip
001-0106-0 (thread 1) skip
001-0107-1 (thread 1) skip
001-0108-0 (thread 1) skip
001-0109-1 (thread 1) skip
001-0110-0 (thread 1) skip
001-0111-1 (thread 1) skip
001-0112-0 (thread 1) skip
001-0113-1 (thread 1) skip
001-0114-0 (thread 1) skip
001-0115-1 (thread 1) skip
001-0116-0 (thread 1) skip
001-0117-1 (thread 1) skip
001-0118-0 (thread 1) skip
001-0119-1 (thread 1) skip
001-0120-0 (thread 1) skip
001-0121-1 (thread 1) skip
001-0122-0 (thread 1) skip
001-0123-1 (thread 1) skip
001-0124-0 (thread 1) skip
001-0125-1 (thread 1) skip
001-0126-0 (thread 1) skip
001-0127-1 (thread 1) skip
001-0128-0 (thread 1) skip
001-0129-1 (thread 1) skip
001-0130-0 (thread 1) skip
001-0131-1 (thread 1) skip
001-0132-0 (thread 1) skip
001-0133-1 (thread 1) skip
001-0134-0 (thread 1) skip
001-0135-1 (thread 1) skip
001-0136-0 (thread 1) skip
001-0137-1 (thread 1) skip
001-0138-0 (thread 1) skip
001-0139-1 (thread 1) skip
001-0140-0 (thread 1) skip
001-0141-1 (thread 1) skip
001-0142-0 (thread 1) skip
001-0143-1 (thread 1) skip
001-0144-0 (thread 1) skip
001-0145-1 (thread 1) skip
001-0146-0 (thread 1) skip
001-0147-1 (thread 1) skip
001-0148-1 (thread 1) identical
001-0148-1 (thread 1) better
|
|
|
6058 Reached 1
|
|
|
6059 done
|
|
|
6060 dvtditr (nuc) Version 7.407
|
|
|
6061 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
6062 1 thread(s)
|
|
|
6063
|
|
|
6064
|
|
|
6065 Strategy:
|
|
|
6066 FFT-NS-i (Standard)
|
|
|
6067 Iterative refinement method (max. 1 iterations)
|
|
|
6068
|
|
|
6069 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
6070 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
6071
|
|
|
6072 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
6073 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
6074 To disable this change, add the --leavegappyregion option.
|
|
|
6075
|
|
|
6076 inputfile = orig
|
|
|
6077 100 x 273 - 156 d
|
|
|
6078 nthread = 1
|
|
|
6079 nthreadpair = 1
|
|
|
6080 nthreadtb = 1
|
|
|
6081 ppenalty_ex = 0
|
|
|
6082 stacksize: 8192 kb
|
|
|
6083 nsubalignments = 2
|
|
|
6084 maxmem = 76
|
|
|
6085 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
6086 Gap Penalty = -1.53, +0.00, +0.00
|
|
|
6087
|
|
|
6088
|
|
|
6089
|
|
|
6090 Making a distance matrix ..
|
|
|
6091
1 / 100 (thread 0)
|
|
|
6092 done.
|
|
|
6093
|
|
|
6094 Constructing a UPGMA tree ...
|
|
|
6095
|
|
|
6096
0 / 100
10 / 100
20 / 100
30 / 100
40 / 100
50 / 100
60 / 100
70 / 100
80 / 100
90 / 100
|
|
|
6097 done.
|
|
|
6098
|
|
|
6099 Checking subalignment 1:
|
|
|
6100 -> OK
|
|
|
6101 Checking subalignment 2:
|
|
|
6102 -> OK
|
|
|
6103 Progressive alignment 1/2...
|
|
|
6104
STEP 99 / 99 (thread 0) f
|
|
|
6105 done.
|
|
|
6106
|
|
|
6107 Making a distance matrix from msa..
|
|
|
6108
0 / 100 (thread 0)
|
|
|
6109 done.
|
|
|
6110
|
|
|
6111 Constructing a UPGMA tree ...
|
|
|
6112
|
|
|
6113
0 / 100
10 / 100
20 / 100
30 / 100
40 / 100
50 / 100
60 / 100
70 / 100
80 / 100
90 / 100
|
|
|
6114 done.
|
|
|
6115
|
|
|
6116 Checking subalignment 1:
|
|
|
6117 -> OK
|
|
|
6118 Checking subalignment 2:
|
|
|
6119 -> OK
|
|
|
6120 Progressive alignment 2/2...
|
|
|
6121
STEP 99 / 99 (thread 0) f
|
|
|
6122 done.
|
|
|
6123
|
|
|
6124 disttbfast (nuc) Version 7.407
|
|
|
6125 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
6126 1 thread(s)
|
|
|
6127
|
|
|
6128 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
6129
0 / 100 (thread 0)dndpre (nuc) Version 7.407
|
|
|
6130 alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0
|
|
|
6131 1 thread(s)
|
|
|
6132
|
|
|
6133 minimumweight = 0.000010
|
|
|
6134 autosubalignment = 0.000000
|
|
|
6135 nthread = 1
|
|
|
6136 randomseed = 0
|
|
|
6137 blosum 62 / kimura 200
|
|
|
6138 poffset = 0
|
|
|
6139 niter = 1
|
|
|
6140 sueff_global = 0.100000
|
|
|
6141 nadd = 1
|
|
|
6142 nsubalignments = 2
|
|
|
6143 maxmem = 76
|
|
|
6144 generating a scoring matrix for nucleotide (dist=200) ... done
|
|
|
6145
|
|
|
6146
|
|
|
6147
0 / 100
10 / 100
20 / 100
30 / 100
40 / 100
50 / 100
60 / 100
70 / 100
80 / 100
90 / 100
|
|
|
6148
|
|
|
6149 Checking subalignment 1:
|
|
|
6150 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76
|
|
|
6151 -> OK
|
|
|
6152
|
|
|
6153 Checking subalignment 2:
|
|
|
6154 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
|
|
|
6155 -> OK
|
|
|
6156 Segment 1/ 1 1- 279
|
|
|
6157 001-0000-0 (thread 1) skip
001-0001-1 (thread 1) skip
001-0002-0 (thread 1) skip
001-0003-1 (thread 1) skip
001-0004-0 (thread 1) skip
001-0005-1 (thread 1) skip
001-0006-0 (thread 1) skip
001-0007-1 (thread 1) skip
001-0008-0 (thread 1) skip
001-0009-1 (thread 1) skip
001-0010-0 (thread 1) skip
001-0011-1 (thread 1) skip
001-0012-0 (thread 1) skip
001-0013-1 (thread 1) skip
001-0014-0 (thread 1) skip
001-0015-1 (thread 1) skip
001-0016-0 (thread 1) skip
001-0017-1 (thread 1) skip
001-0018-0 (thread 1) skip
001-0019-1 (thread 1) skip
001-0020-0 (thread 1) skip
001-0021-1 (thread 1) skip
001-0022-0 (thread 1) skip
001-0023-1 (thread 1) skip
001-0024-0 (thread 1) skip
001-0025-1 (thread 1) skip
001-0026-0 (thread 1) skip
001-0027-1 (thread 1) skip
001-0028-0 (thread 1) skip
001-0029-1 (thread 1) skip
001-0030-0 (thread 1) skip
001-0031-1 (thread 1) skip
001-0032-0 (thread 1) skip
001-0033-1 (thread 1) skip
001-0034-0 (thread 1) skip
001-0035-1 (thread 1) skip
001-0036-0 (thread 1) skip
001-0037-1 (thread 1) skip
001-0038-0 (thread 1) skip
001-0039-1 (thread 1) skip
001-0040-0 (thread 1) skip
001-0041-1 (thread 1) skip
001-0042-0 (thread 1) skip
001-0043-1 (thread 1) skip
001-0044-0 (thread 1) skip
001-0045-1 (thread 1) skip
001-0046-0 (thread 1) skip
001-0047-1 (thread 1) skip
001-0048-0 (thread 1) skip
001-0049-1 (thread 1) skip
001-0050-0 (thread 1) skip
001-0051-1 (thread 1) skip
001-0052-0 (thread 1) skip
001-0053-1 (thread 1) skip
001-0054-0 (thread 1) skip
001-0055-1 (thread 1) skip
001-0056-0 (thread 1) skip
001-0057-1 (thread 1) skip
001-0058-0 (thread 1) skip
001-0059-1 (thread 1) skip
001-0060-0 (thread 1) skip
001-0061-1 (thread 1) skip
001-0062-0 (thread 1) skip
001-0063-1 (thread 1) skip
001-0064-0 (thread 1) skip
001-0065-1 (thread 1) skip
001-0066-0 (thread 1) skip
001-0067-1 (thread 1) skip
001-0068-0 (thread 1) skip
001-0069-1 (thread 1) skip
001-0070-0 (thread 1) skip
001-0071-1 (thread 1) skip
001-0072-0 (thread 1) skip
001-0073-1 (thread 1) skip
001-0074-0 (thread 1) skip
001-0075-1 (thread 1) skip
001-0076-0 (thread 1) skip
001-0077-1 (thread 1) skip
001-0078-0 (thread 1) skip
001-0079-1 (thread 1) skip
001-0080-0 (thread 1) skip
001-0081-1 (thread 1) skip
001-0082-0 (thread 1) skip
001-0083-1 (thread 1) skip
001-0084-0 (thread 1) skip
001-0085-1 (thread 1) skip
001-0086-0 (thread 1) skip
001-0087-1 (thread 1) skip
001-0088-0 (thread 1) skip
001-0089-1 (thread 1) skip
001-0090-0 (thread 1) skip
001-0091-1 (thread 1) skip
001-0092-0 (thread 1) skip
001-0093-1 (thread 1) skip
001-0094-0 (thread 1) skip
001-0095-1 (thread 1) skip
001-0096-0 (thread 1) skip
001-0097-1 (thread 1) skip
001-0098-0 (thread 1) skip
001-0099-1 (thread 1) skip
001-0100-0 (thread 1) skip
001-0101-1 (thread 1) skip
001-0102-0 (thread 1) skip
001-0103-1 (thread 1) skip
001-0104-0 (thread 1) skip
001-0105-1 (thread 1) skip
001-0106-0 (thread 1) skip
001-0107-1 (thread 1) skip
001-0108-0 (thread 1) skip
001-0109-1 (thread 1) skip
001-0110-0 (thread 1) skip
001-0111-1 (thread 1) skip
001-0112-0 (thread 1) skip
001-0113-1 (thread 1) skip
001-0114-0 (thread 1) skip
001-0115-1 (thread 1) skip
001-0116-0 (thread 1) skip
001-0117-1 (thread 1) skip
001-0118-0 (thread 1) skip
001-0119-1 (thread 1) skip
001-0120-0 (thread 1) skip
001-0121-1 (thread 1) skip
001-0122-0 (thread 1) skip
001-0123-1 (thread 1) skip
001-0124-0 (thread 1) skip
001-0125-1 (thread 1) skip
001-0126-0 (thread 1) skip
001-0127-1 (thread 1) skip
001-0128-0 (thread 1) skip
001-0129-1 (thread 1) skip
001-0130-0 (thread 1) skip
001-0131-1 (thread 1) skip
001-0132-0 (thread 1) skip
001-0133-1 (thread 1) skip
001-0134-0 (thread 1) skip
001-0135-1 (thread 1) skip
001-0136-0 (thread 1) skip
001-0137-1 (thread 1) skip
001-0138-0 (thread 1) skip
001-0139-1 (thread 1) skip
001-0140-0 (thread 1) skip
001-0141-1 (thread 1) skip
001-0142-0 (thread 1) skip
001-0143-1 (thread 1) skip
001-0144-0 (thread 1) skip
001-0145-1 (thread 1) skip
001-0146-0 (thread 1) skip
001-0147-1 (thread 1) skip
001-0148-0 (thread 1) skip
001-0149-1 (thread 1) skip
001-0150-0 (thread 1) skip
001-0151-1 (thread 1) skip
001-0152-0 (thread 1) skip
001-0153-1 (thread 1) skip
001-0154-0 (thread 1) skip
001-0155-1 (thread 1) skip
001-0156-0 (thread 1) skip
001-0157-1 (thread 1) skip
001-0158-0 (thread 1) skip
001-0159-1 (thread 1) skip
001-0160-0 (thread 1) skip
001-0161-1 (thread 1) skip
001-0162-0 (thread 1) skip
001-0163-1 (thread 1) skip
001-0164-0 (thread 1) skip
001-0165-1 (thread 1) skip
001-0166-0 (thread 1) skip
001-0167-1 (thread 1) skip
001-0168-0 (thread 1) skip
001-0169-1 (thread 1) skip
001-0170-0 (thread 1) skip
001-0171-1 (thread 1) skip
001-0172-0 (thread 1) skip
001-0173-1 (thread 1) skip
001-0174-0 (thread 1) skip
001-0175-1 (thread 1) skip
001-0176-0 (thread 1) skip
001-0177-1 (thread 1) skip
001-0178-0 (thread 1) skip
001-0179-1 (thread 1) skip
001-0180-0 (thread 1) skip
001-0181-1 (thread 1) skip
001-0182-0 (thread 1) skip
001-0183-1 (thread 1) skip
001-0184-0 (thread 1) skip
001-0185-1 (thread 1) skip
001-0186-0 (thread 1) skip
001-0187-1 (thread 1) skip
001-0188-0 (thread 1) skip
001-0189-1 (thread 1) skip
001-0190-0 (thread 1) skip
001-0191-1 (thread 1) skip
001-0192-0 (thread 1) skip
001-0193-1 (thread 1) skip
001-0194-0 (thread 1) skip
001-0195-1 (thread 1) skip
001-0196-1 (thread 1) identical
001-0196-1 (thread 1) worse
|
|
|
6158 Converged.
|
|
|
6159
|
|
|
6160 Reached 1
|
|
|
6161 done
|
|
|
6162 dvtditr (nuc) Version 7.407
|
|
|
6163 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
6164 1 thread(s)
|
|
|
6165
|
|
|
6166
|
|
|
6167 Strategy:
|
|
|
6168 FFT-NS-i (Standard)
|
|
|
6169 Iterative refinement method (max. 1 iterations)
|
|
|
6170
|
|
|
6171 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
6172 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
6173
|
|
|
6174 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
6175 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
6176 To disable this change, add the --leavegappyregion option.
|
|
|
6177
|
