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0
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1 inputfile = orig
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2 2 x 70 - 70 d
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3 outputhat23=1
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4 treein = 0
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5 compacttree = 0
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6 stacksize: 8192 kb
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7 generating a scoring matrix for nucleotide (dist=200) ... done
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8 All-to-all alignment.
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9 0 / 2 (by thread 0)
tbfast-pair (nuc) Version 7.407
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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)
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12
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13 outputhat23=1
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14 Loading 'hat3.seed' ...
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15 done.
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16 Writing hat3 for iterative refinement
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17 generating a scoring matrix for nucleotide (dist=200) ... done
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18 Gap Penalty = -1.53, +0.00, +0.00
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19 tbutree = 1, compacttree = 0
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20 Constructing a UPGMA tree ...
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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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26 done.
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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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30
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31 minimumweight = 0.000010
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32 autosubalignment = 0.000000
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33 nthread = 1
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34 randomseed = 0
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35 blosum 62 / kimura 200
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36 poffset = 0
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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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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- 86
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45 001-0000-1 (thread 1) identical
001-0000-1 (thread 1) better
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46 Reached 1
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47 done
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48 dvtditr (nuc) Version 7.407
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49 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
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50 1 thread(s)
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51
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52
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53 Strategy:
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54 L-INS-i (Probably most accurate, very slow)
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55 Iterative refinement method (<1) with LOCAL pairwise alignment information
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56
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57 If unsure which option to use, try 'mafft --auto input > output'.
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58 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
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59
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60 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
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61 It tends to insert more gaps into gap-rich regions than previous versions.
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62 To disable this change, add the --leavegappyregion option.
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63
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