Mercurial > repos > dave > pipelign
diff test-data/files/merge.log @ 0:9a3a2e04f47a draft default tip
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| author | dave |
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| date | Mon, 10 Jun 2019 16:04:10 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/merge.log Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,6177 @@ +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 72 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 70 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 83 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 91 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 108 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 92 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 76 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 118 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 115 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 94 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 87 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 80 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 84 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 82 - 75 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 91 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 78 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 73 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 84 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 88 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 105 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 77 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 76 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 79 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 80 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 97 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 72 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 97 +001-0000-1 (thread 1) identical 001-0000-1 (thread 1) better +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 89 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 95 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +2 x 70 - 70 d +outputhat23=1 +treein = 0 +compacttree = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 0 / 2 (by thread 0) tbfast-pair (nuc) Version 7.407 +alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +outputhat23=1 +Loading 'hat3.seed' ... +done. +Writing hat3 for iterative refinement +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 +tbutree = 1, compacttree = 0 +Constructing a UPGMA tree ... + 0 / 2 +done. + +Progressive alignment ... + STEP 1 /1 (thread 0) +done. +tbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +Loading 'hat3' ... done. +generating a scoring matrix for nucleotide (dist=200) ... done + + 0 / 2 +Segment 1/ 1 1- 95 +001-0000-1 (thread 1) identical +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + L-INS-i (Probably most accurate, very slow) + Iterative refinement method (<1) with LOCAL pairwise alignment information + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 71 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 110 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 4 +njobc = 5 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 90 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 107 - 99 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### +Reallocated inconsistentpairlist, size=2 + +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 156 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 91 - 78 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 + -> OK +Segment 1/ 1 1- 108 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 117 - 114 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 2 1- 62 +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 +Converged. + +Reached 1 +Segment 2/ 2 62- 134 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 78 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 102 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 84 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 4 +njobc = 5 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +3 x 72 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 2 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 2 +njobc = 3 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 99 - 76 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### + +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 103 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 101 - 72 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 + -> OK +Segment 1/ 1 1- 102 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 95 - 71 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 3 / 3 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 4 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 4 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 3 / 3 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 4 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 2 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 4 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 + -> OK +Segment 1/ 1 1- 114 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 102 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 115 - 96 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 6 + -> OK +Segment 1/ 1 1- 154 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 110 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 5 +njobc = 6 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +4 x 108 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 3 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 3 +njobc = 4 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 93 - 87 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 + -> OK +Segment 1/ 1 1- 102 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 98 - 87 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 7 / 7 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 7 / 7 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 8 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 6 7 8 + -> OK +Segment 1/ 1 1- 105 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +5 x 97 - 74 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 4 / 4 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 5 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 4 / 4 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 3 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 5 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 + -> OK +Segment 1/ 1 1- 109 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 106 - 87 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 + -> OK +Segment 1/ 1 1- 127 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 101 - 91 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 7 / 7 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 7 / 7 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 5 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 8 + +Checking subalignment 1: + 1 2 3 4 5 + -> OK + +Checking subalignment 2: + 6 7 8 + -> OK +Segment 1/ 1 1- 102 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 99 - 85 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### +Reallocated inconsistentpairlist, size=2 + +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 + -> OK +Segment 1/ 1 1- 123 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 115 - 94 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 5 / 5 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 6 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 6 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 5 / 5 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 4 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 6 + +Checking subalignment 1: + 1 2 3 4 + -> OK + +Checking subalignment 2: + 5 6 + -> OK +Segment 1/ 1 1- 141 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +7 x 120 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 6 +njobc = 7 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 99 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 5 +njobc = 6 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +9 x 104 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 8 +njobc = 9 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +6 x 108 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 5 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 5 +njobc = 6 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 126 - 83 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 7 / 7 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 8 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 8 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 7 / 7 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 8 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 8 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 7 8 + -> OK +Segment 1/ 1 1- 130 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +7 x 100 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 6 +njobc = 7 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +7 x 140 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 6 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 6 +njobc = 7 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +13 x 128 - 123 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 13 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 13 10 / 13 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 12 / 12 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 13 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 13 10 / 13 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 12 / 12 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 13 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 13 10 / 13 + +Checking subalignment 1: + 1 2 3 4 5 6 + -> OK + +Checking subalignment 2: + 7 8 9 10 11 12 13 + -> OK +Segment 1/ 1 1- 163 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +10 x 130 - 111 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 9 / 9 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 9 / 9 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 6 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 10 + +Checking subalignment 1: + 1 2 3 4 + -> OK + +Checking subalignment 2: + 5 6 7 8 9 10 + -> OK +Segment 1/ 1 1- 142 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +16 x 129 - 101 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 16 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 16 10 / 16 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 15 / 15 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 16 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 16 10 / 16 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 15 / 15 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 16 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 16 10 / 16 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 + -> OK + +Checking subalignment 2: + 9 10 11 12 13 14 15 16 + -> OK +Segment 1/ 1 1- 152 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +10 x 108 - 96 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 9 / 9 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 9 / 9 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 7 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 10 + +Checking subalignment 1: + 1 2 3 + -> OK + +Checking subalignment 2: + 4 5 6 7 8 9 10 + -> OK +Segment 1/ 1 1- 122 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +8 x 140 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 7 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 7 +njobc = 8 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +17 x 151 - 113 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 17 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 17 10 / 17 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 16 / 16 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 17 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 17 10 / 17 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 16 / 16 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 17 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 17 10 / 17 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 + -> OK + +Checking subalignment 2: + 14 15 16 17 + -> OK +Segment 1/ 1 1- 166 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +11 x 141 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 10 +njobc = 11 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +22 x 157 - 112 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 16 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 22 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 22 10 / 22 20 / 22 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 21 / 21 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 22 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 22 10 / 22 20 / 22 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 21 / 21 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 22 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 16 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 22 10 / 22 20 / 22 + +Checking subalignment 1: + 1 2 3 4 5 6 + -> OK + +Checking subalignment 2: + 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + -> OK +Segment 1/ 1 1- 170 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +12 x 121 - 96 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 10 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 12 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 12 +################################################################### +# WARNING: Group 2 is forced to be a monophyletic cluster. +################################################################### +Reallocated inconsistentpairlist, size=2 + 10 / 12 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 11 / 11 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 12 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 12 10 / 12 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 11 / 11 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 12 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 10 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 12 10 / 12 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 + -> OK + +Checking subalignment 2: + 11 12 + -> OK +Segment 1/ 1 1- 122 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +10 x 142 - 88 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 9 / 9 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 10 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 10 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 9 / 9 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 10 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 8 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 10 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 7 8 9 10 + -> OK +Segment 1/ 1 1- 157 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +21 x 168 - 155 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 17 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 21 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 21 10 / 21 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 20 / 20 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 21 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 21 10 / 21 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 20 / 20 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 21 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 17 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 21 10 / 21 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 + -> OK + +Checking subalignment 2: + 18 19 20 21 + -> OK +Segment 1/ 1 1- 209 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +12 x 141 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 11 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + 10 / 11 (by thread 0) + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 11 +njobc = 12 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +24 x 169 - 74 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 22 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 24 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 24 10 / 24 20 / 24 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 23 / 23 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 24 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 24 10 / 24 20 / 24 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 23 / 23 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 24 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 22 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 24 10 / 24 20 / 24 + +Checking subalignment 1: + 1 2 + -> OK + +Checking subalignment 2: + 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + -> OK +Segment 1/ 1 1- 174 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +13 x 121 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 12 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 12 +njobc = 13 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +26 x 186 - 107 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 21 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 26 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 26 10 / 26 20 / 26 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 25 / 25 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 26 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 26 10 / 26 20 / 26 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 25 / 25 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 26 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 21 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 26 10 / 26 20 / 26 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 + -> OK + +Checking subalignment 2: + 22 23 24 25 26 + -> OK +Segment 1/ 1 1- 199 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +25 x 173 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 24 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 24 +njobc = 25 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +23 x 142 - 130 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 23 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 23 10 / 23 20 / 23 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 22 / 22 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 23 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 23 10 / 23 20 / 23 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 22 / 22 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 23 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 13 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 23 10 / 23 20 / 23 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 10 11 12 13 + -> OK + +Checking subalignment 2: + 14 15 16 17 18 19 20 21 22 23 + -> OK +Segment 1/ 1 1- 155 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +38 x 198 - 155 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 26 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 37 / 37 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 37 / 37 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 38 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 26 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 38 10 / 38 20 / 38 30 / 38 + +Checking subalignment 1: + 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 + -> OK + +Checking subalignment 2: + 27 28 29 30 31 32 33 34 35 36 37 38 + -> OK +Segment 1/ 1 1- 205 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +34 x 182 - 104 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 25 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 34 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 34 10 / 34 20 / 34 30 / 34 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 33 / 33 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 34 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 34 10 / 34 20 / 34 30 / 34 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 33 / 33 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 34 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 25 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 34 10 / 34 20 / 34 30 / 34 + +Checking subalignment 1: + 1 2 3 4 5 6 7 8 9 + -> OK + +Checking subalignment 2: + 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 + -> OK +Segment 1/ 1 1- 188 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +24 x 154 - 70 d +nadd = 1 +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 23 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done +All-to-all alignment. + + +##### writing hat3 +pairlocalalign (nuc) Version 7.407 +alg=Y, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 +1 thread(s) + +nadd = 1 +ppenalty_ex = -10 +nthread = 1 +blosum 62 / kimura 200 +sueff_global = 0.100000 +norg = 23 +njobc = 24 +Loading 'hat3' ... +done. +generating a scoring matrix for nucleotide (dist=200) ... done +Loading 'hat2n' (aligned sequences - new sequences) ... done. +Loading 'hat2i' (aligned sequences) ... done. + 0 / 1 (thread 0) c + +Combining .. +0 / 1 0 / 1 done. + + done. + +addsingle (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + Multi-INS-fragment (Not tested.) + ? + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +38 x 187 - 149 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 34 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 37 / 37 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 38 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 38 10 / 38 20 / 38 30 / 38 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 37 / 37 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 38 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 34 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 38 10 / 38 20 / 38 30 / 38 + +Checking subalignment 1: + 1 2 3 4 + -> OK + +Checking subalignment 2: + 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 + -> OK +Segment 1/ 1 1- 216 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +76 x 215 - 206 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 38 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 76 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 76 10 / 76 20 / 76 30 / 76 40 / 76 50 / 76 60 / 76 70 / 76 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 75 / 75 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 76 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 76 10 / 76 20 / 76 30 / 76 40 / 76 50 / 76 60 / 76 70 / 76 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 75 / 75 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 76 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 38 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 76 10 / 76 20 / 76 30 / 76 40 / 76 50 / 76 60 / 76 70 / 76 + +Checking subalignment 1: + 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 + -> OK + +Checking subalignment 2: + 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 + -> OK +Segment 1/ 1 1- 285 +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 +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. + +inputfile = orig +100 x 273 - 156 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +nsubalignments = 2 +maxmem = 76 +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 100 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 100 10 / 100 20 / 100 30 / 100 40 / 100 50 / 100 60 / 100 70 / 100 80 / 100 90 / 100 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 1/2... + STEP 99 / 99 (thread 0) f +done. + +Making a distance matrix from msa.. + 0 / 100 (thread 0) +done. + +Constructing a UPGMA tree ... + + 0 / 100 10 / 100 20 / 100 30 / 100 40 / 100 50 / 100 60 / 100 70 / 100 80 / 100 90 / 100 +done. + +Checking subalignment 1: + -> OK +Checking subalignment 2: + -> OK +Progressive alignment 2/2... + STEP 99 / 99 (thread 0) f +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + +generating a scoring matrix for nucleotide (dist=200) ... done + 0 / 100 (thread 0)dndpre (nuc) Version 7.407 +alg=X, model=DNA200 (2), 1.53 (4.59), 0.37 (1.11), noshift, amax=0.0 +1 thread(s) + +minimumweight = 0.000010 +autosubalignment = 0.000000 +nthread = 1 +randomseed = 0 +blosum 62 / kimura 200 +poffset = 0 +niter = 1 +sueff_global = 0.100000 +nadd = 1 +nsubalignments = 2 +maxmem = 76 +generating a scoring matrix for nucleotide (dist=200) ... done + + + 0 / 100 10 / 100 20 / 100 30 / 100 40 / 100 50 / 100 60 / 100 70 / 100 80 / 100 90 / 100 + +Checking subalignment 1: + 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 + -> OK + +Checking subalignment 2: + 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 + -> OK +Segment 1/ 1 1- 279 +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 +Converged. + +Reached 1 +done +dvtditr (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-i (Standard) + Iterative refinement method (max. 1 iterations) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +