Mercurial > repos > iuc > trimal
changeset 0:ebe28cac8d8b draft
planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
| author | iuc |
|---|---|
| date | Fri, 15 Nov 2024 08:59:26 +0000 |
| parents | |
| children | 2a156ec81e7a |
| files | README.md test-data/custom_trimmed_example.009.AA.html test-data/custom_trimmed_example.009.AA.phy test-data/example.004.AA.fasta test-data/example.009.AA.fasta test-data/trimmed_example.009.AA.html test-data/trimmed_example.009.AA.mega trimal.xml |
| diffstat | 8 files changed, 411 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,3 @@ +# trimAl + +[trimAl](https://github.com/inab/trimal), a tool for automated alignment trimming in large-scale phylogenetic analyses.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_example.009.AA.html Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,74 @@ +<!DOCTYPE html> +<html><head> + <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" /> + <title>trimAl v1.5.0 Summary</title> + <style type="text/css" media="all"> + #b { background-color: #3366ff; } + #r { background-color: #cc0000; } + #g { background-color: #33cc00; } + #p { background-color: #ff6666; } + #m { background-color: #cc33cc; } + #o { background-color: #ff9900; } + #c { background-color: #46C7C7; } + #y { background-color: #FFFF00; } + .sel { background-color: #B9B9B9; } + .nsel { background-color: #E9E9E9; } + .c1 { background-color: #FFFBF2; } + .c2 { background-color: #FFF8CC; } + .c3 { background-color: #FAF0BE; } + .c4 { background-color: #F0EAD6; } + .c5 { background-color: #F3E5AB; } + .c6 { background-color: #F4C430; } + .c7 { background-color: #C2B280; color: white; } + .c8 { background-color: #DAA520; color: white; } + .c9 { background-color: #B8860B; color: white; } + .c10 { background-color: #918151; color: white; } + .c11 { background-color: #967117; color: white; } + .c12 { background-color: #6E5411; color: white; } + </style> + </head> + + <body> + <pre> + <span class=sel>Selected Sequences: 9 /Selected Residues: 63</span> + <span class=nsel>Deleted Sequences: 0 /Deleted Residues: 122</span> + + Gaps Scores: <span class=c1> =0= </span><span class=c2> <.001 </span><span class=c3> <.050 </span><span class=c4> <.100 </span><span class=c5> <.150 </span><span class=c6> <.200 </span><span class=c7> <.250 </span><span class=c8> <.350 </span><span class=c9> <.500 </span><span class=c10> <.750 </span><span class=c11> <1.00 </span><span class=c12> =1= </span> + Similarity Scores: <span class=c1> =0= </span><span class=c2> <1e-6 </span><span class=c3> <1e-5 </span><span class=c4> <1e-4 </span><span class=c5> <.001 </span><span class=c6> <.010 </span><span class=c7> <.100 </span><span class=c8> <.250 </span><span class=c9> <.500 </span><span class=c10> <.750 </span><span class=c11> <1.00 </span><span class=c12> =1= </span> + + 10 20 30 40 50 60 70 80 90 100 110 120 + =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+ + <span class=sel>Csa004271</span> ---------------------------------M<span id=c>Y</span>M<span id=b>A</span><span id=b>M</span><span id=o>G</span><span id=c>H</span><span id=b>F</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span>KN<span id=b>I</span>SE<span id=c>Y</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>C<span id=g>S</span>E<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span>N<span id=r>K</span><span id=b>M</span><span id=b>I</span>E<span id=b>F</span>H<span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span>T<span id=g>T</span><span id=g>T</span><span id=c>Y</span>F<span id=y>P</span><span id=b>I</span><span id=r>K</span>A<span id=y>P</span><span id=o>G</span>SF<span id=m>D</span><span id=y>P</span>ANFNT<span id=b>I</span>K<span id=b>A</span><span id=b>M</span>N<span id=b>C</span><span id=b>A</span><span id=b>L</span>A<span id=b>L</span><span id=m>E</span>V<span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=r>K</span>S<span id=b>L</span><span id=b>L</span>A<span id=b>L</span> + <span class=sel>Xtr21234</span> ----MI<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span>SH<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>V</span><span id=g>N</span><span id=r>R</span>M<span id=b>V</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>M</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>S<span id=c>H</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=c>H</span>H<span id=b>V</span><span id=b>A</span>E<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>Q<span id=g>S</span>K<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>C</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>V</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span>T<span id=b>L</span><span id=m>D</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=g>T</span><span id=b>A</span><span id=b>L</span>D<span id=b>L</span><span id=m>E</span><span id=r>K</span>H<span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>LcaH</span> ----MS<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=b>F</span><span id=c>H</span>Q<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>Q<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span>V<span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>A<span id=c>Y</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span>Q<span id=b>A</span><span id=b>L</span><span id=c>H</span>N<span id=b>F</span><span id=b>A</span>K<span id=b>F</span><span id=b>F</span><span id=r>R</span>HQ<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>L</span><span id=g>Q</span><span id=g>N</span><span id=g>Q</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>V</span><span id=r>R</span><span id=r>K</span><span id=y>P</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>L</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span>S<span id=b>V</span><span id=g>N</span><span id=g>Q</span>S<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>Hsa167996</span> MTTAST<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>Q<span id=m>D</span>S<span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>Q<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span>V<span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>S<span id=c>Y</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span>KN<span id=b>F</span><span id=b>A</span>K<span id=c>Y</span><span id=b>F</span>LHQ<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>L</span><span id=g>Q</span><span id=g>N</span><span id=g>Q</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>D</span>C<span id=m>D</span><span id=m>D</span><span id=b>W</span>E--<span id=g>S</span><span id=o>G</span><span id=b>L</span>N<span id=b>A</span><span id=b>M</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=b>L</span>H<span id=b>L</span><span id=m>E</span><span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>S<span id=b>L</span><span id=b>L</span><span id=m>E</span><span id=b>L</span> + <span class=sel>Mmu024661</span> MTTAS<span id=y>P</span><span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>Q<span id=m>D</span><span id=b>A</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>Q<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span>V<span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>S<span id=b>C</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span>KN<span id=b>F</span><span id=b>A</span>K<span id=c>Y</span><span id=b>F</span>LHQ<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>L</span><span id=g>Q</span><span id=g>N</span><span id=g>Q</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>W</span>E--<span id=g>S</span><span id=o>G</span><span id=b>L</span>N<span id=b>A</span><span id=b>M</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=b>L</span>H<span id=b>L</span><span id=m>E</span><span id=r>K</span>S<span id=b>V</span><span id=g>N</span><span id=g>Q</span>S<span id=b>L</span><span id=b>L</span><span id=m>E</span><span id=b>L</span> + <span class=sel>Dre37936</span> ---MET<span id=g>S</span><span id=g>Q</span><span id=b>I</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=b>V</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>K</span>M<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=o>G</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=c>H</span><span id=c>Y</span><span id=b>F</span>K<span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span><span id=b>A</span>K<span id=b>F</span><span id=b>F</span><span id=r>K</span>KN<span id=g>S</span>E<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>F</span><span id=b>M</span>E<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>V</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>D</span><span id=r>R</span><span id=m>D</span>V<span id=b>W</span><span id=o>G</span>--N<span id=o>G</span><span id=b>L</span>I<span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>LcaM</span> ----ME<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>V</span><span id=g>N</span><span id=r>R</span>M<span id=b>V</span><span id=g>N</span><span id=b>M</span><span id=m>E</span><span id=b>M</span><span id=b>F</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=b>F</span><span id=c>Y</span><span id=b>F</span>S<span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span>SH<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>N<span id=g>S</span>D<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>L</span>S<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span>H<span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span>K<span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>Tru14292</span> ----ME<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>K</span>M<span id=b>I</span><span id=g>N</span><span id=b>M</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=b>F</span><span id=b>F</span><span id=b>F</span>S<span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span><span id=b>A</span>H<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>N<span id=g>S</span>D<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>L</span>S<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span>K<span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>Ola20972</span> ----ME<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>M<span id=b>V</span><span id=g>N</span><span id=b>M</span><span id=m>E</span><span id=b>L</span><span id=b>F</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=b>F</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span>SH<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>N<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>K</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>D</span><span id=r>K</span><span id=b>L</span><span id=b>L</span>S<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>V</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + + Selected Cols: <span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span> + + Gaps Scores: <span class=c7> </span><span class=c7> </span><span class=c7> </span><span class=c8> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c5> </span><span class=c5> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span> + Similarity Scores: <span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c5> </span><span class=c5> </span><span class=c4> </span><span class=c12> </span><span class=c12> </span><span class=c9> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c8> </span><span class=c5> </span><span class=c6> </span><span class=c12> </span><span class=c6> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c8> </span><span class=c12> </span><span class=c8> </span><span class=c5> </span><span class=c8> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c7> </span><span class=c7> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c5> </span><span class=c12> </span><span class=c5> </span><span class=c7> </span><span class=c12> </span><span class=c6> </span><span class=c4> </span><span class=c7> </span><span class=c12> </span><span class=c6> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c12> </span><span class=c4> </span><span class=c5> </span><span class=c6> </span><span class=c7> </span><span class=c5> </span><span class=c7> </span><span class=c12> </span><span class=c6> </span><span class=c5> </span><span class=c4> </span><span class=c12> </span><span class=c5> </span><span class=c12> </span><span class=c12> </span><span class=c9> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c7> </span><span class=c7> </span><span class=c6> </span><span class=c5> </span><span class=c7> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c6> </span><span class=c7> </span><span class=c5> </span><span class=c6> </span><span class=c6> </span><span class=c7> </span><span class=c9> </span><span class=c9> </span><span class=c7> </span><span class=c12> </span><span class=c5> </span><span class=c6> </span><span class=c5> </span><span class=c6> </span><span class=c5> </span><span class=c5> </span><span class=c1> </span><span class=c1> </span><span class=c7> </span><span class=c6> </span><span class=c7> </span><span class=c5> </span><span class=c12> </span><span class=c9> </span><span class=c6> </span><span class=c7> </span><span class=c12> </span><span class=c12> </span><span class=c4> </span><span class=c12> </span><span class=c9> </span><span class=c6> </span><span class=c6> </span><span class=c12> </span><span class=c12> </span><span class=c7> </span><span class=c7> </span><span class=c12> </span><span class=c12> </span><span class=c6> </span><span class=c12> </span> + + 130 140 150 160 170 180 + =========+=========+=========+=========+=========+=========+===== + <span class=sel>Csa004271</span> <span id=c>H</span>E--<span id=g>T</span>AN<span id=o>G</span><span id=m>D</span><span id=y>P</span>E<span id=b>F</span>Q<span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span>AN<span id=b>F</span><span id=b>L</span>H<span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>D</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span>K<span id=m>D</span><span id=c>Y</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>KL<span id=b>V</span><span id=o>G</span>---T<span id=o>G</span><span id=b>L</span><span id=o>G</span><span id=m>E</span><span id=b>F</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span>FKSS----- + <span class=sel>Xtr21234</span> <span id=c>H</span>N<span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>E</span>RK<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>I</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>S</span>E<span id=c>H</span><span id=b>L</span><span id=m>D</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span>K<span id=c>H</span><span id=b>M</span><span id=r>K</span><span id=r>K</span><span id=b>F</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>K<span id=r>R</span><span id=b>L</span><span id=o>G</span><span id=b>V</span><span id=y>P</span>Q<span id=g>N</span><span id=o>G</span><span id=b>M</span><span id=o>G</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>S</span><span id=b>L</span>S------ + <span class=sel>LcaH</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>C</span><span id=g>S</span><span id=m>D</span><span id=c>H</span>N<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=m>D</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span>KS<span id=b>I</span><span id=r>K</span>E<span id=b>L</span>A<span id=m>D</span><span id=b>W</span><span id=b>V</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>R<span id=r>R</span><span id=b>M</span><span id=o>G</span><span id=b>A</span><span id=y>P</span>Q<span id=g>N</span><span id=o>G</span><span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>KES--S + <span class=sel>Hsa167996</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>D</span>KN<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span>K<span id=b>A</span><span id=b>I</span><span id=r>K</span>E<span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>V</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>R<span id=r>K</span><span id=b>M</span><span id=o>G</span><span id=b>A</span><span id=y>P</span>ES<span id=o>G</span><span id=b>L</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>DSDNES + <span class=sel>Mmu024661</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>D</span>KN<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span><span id=g>T</span><span id=c>Y</span><span id=c>Y</span><span id=b>L</span>S<span id=m>E</span><span id=g>Q</span><span id=b>V</span>KS<span id=b>I</span><span id=r>K</span>E<span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>V</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>R<span id=r>K</span><span id=b>M</span><span id=o>G</span><span id=b>A</span><span id=y>P</span>EA<span id=o>G</span><span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>H<span id=o>G</span>D-ES + <span class=sel>Dre37936</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>E</span>M<span id=o>G</span><span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>S<span id=r>K</span><span id=b>M</span>D<span id=b>A</span><span id=o>G</span>N<span id=g>N</span>R<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span>DS----- + <span class=sel>LcaM</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>S</span><span id=m>D</span><span id=c>H</span><span id=o>G</span><span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>Y</span><span id=b>I</span><span id=g>S</span><span id=g>N</span><span id=b>L</span>S<span id=r>R</span><span id=b>M</span>D<span id=b>A</span>QK<span id=g>N</span>K<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>S</span><span id=b>L</span><span id=o>G</span><span id=o>G</span>KS--- + <span class=sel>Tru14292</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>S</span><span id=m>D</span><span id=c>H</span>V<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>S</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>Y</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>S<span id=r>R</span><span id=b>M</span>D<span id=b>A</span>QN<span id=g>N</span>K<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>SKS--- + <span class=sel>Ola20972</span> <span id=c>H</span><span id=r>K</span><span id=b>V</span><span id=b>A</span><span id=g>S</span><span id=m>D</span><span id=c>H</span>K<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>M</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span>S<span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>I</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>T<span id=r>R</span><span id=b>M</span>D<span id=b>A</span><span id=c>H</span>T<span id=g>N</span>K<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>SKS--- + + Selected Cols: <span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span> + + Gaps Scores: <span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c10> </span><span class=c10> </span><span class=c5> </span><span class=c7> </span><span class=c8> </span> + Similarity Scores: <span class=c12> </span><span class=c7> </span><span class=c9> </span><span class=c7> </span><span class=c7> </span><span class=c6> </span><span class=c4> </span><span class=c4> </span><span class=c12> </span><span class=c12> </span><span class=c7> </span><span class=c6> </span><span class=c6> </span><span class=c12> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c7> </span><span class=c5> </span><span class=c6> </span><span class=c12> </span><span class=c5> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c6> </span><span class=c6> </span><span class=c8> </span><span class=c12> </span><span class=c7> </span><span class=c7> </span><span class=c6> </span><span class=c12> </span><span class=c5> </span><span class=c8> </span><span class=c9> </span><span class=c12> </span><span class=c12> </span><span class=c5> </span><span class=c5> </span><span class=c7> </span><span class=c5> </span><span class=c7> </span><span class=c4> </span><span class=c5> </span><span class=c6> </span><span class=c5> </span><span class=c7> </span><span class=c6> </span><span class=c12> </span><span class=c7> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c5> </span><span class=c6> </span><span class=c6> </span><span class=c5> </span><span class=c5> </span><span class=c6> </span><span class=c1> </span><span class=c12> </span><span class=c12> </span> + </pre> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_example.009.AA.phy Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,11 @@ + 9 63 +Csa004271 --------------YMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +Xtr21234 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +LcaH SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +Hsa167996 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +Mmu024661 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +Dre37936 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +LcaM SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +Tru14292 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +Ola20972 SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.004.AA.fasta Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,18 @@ +>Sp8 +FPWNGLQIHMMGIII + +>Sp17 +FPWNGLQIHMMGIII + +>Sp10 +FPWNGLQIHMMGIII + +>Sp26 +FPWNGLQIHMMGIII + +>Sp33 +FPWNGLQIHMMGIII + +>Sp6 +FPWNGLQIHMMGIII +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.009.AA.fasta Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,45 @@ +>Csa004271 +---------------------------------MYMAMGHFFDRDDVALKNISEYFKECS +EEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL +HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS +----- +>Xtr21234 +----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQS +KEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL +HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS- +----- +>LcaH +----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQS +HEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL +HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGK +ES--S +>Hsa167996 +MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS +HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL +HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGD +SDNES +>Mmu024661 +MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQS +HEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL +HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGH +GD-ES +>Dre37936 +---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNS +EEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL +HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS +----- +>LcaM +----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENS +DEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL +HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGG +KS--- +>Tru14292 +----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENS +DEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL +HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGS +KS--- +>Ola20972 +----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENS +HEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL +HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGS +KS--- \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmed_example.009.AA.html Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,71 @@ +<!DOCTYPE html> +<html><head> + <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" /> + <title>trimAl v1.5.0 Summary</title> + <style type="text/css" media="all"> + #b { background-color: #3366ff; } + #r { background-color: #cc0000; } + #g { background-color: #33cc00; } + #p { background-color: #ff6666; } + #m { background-color: #cc33cc; } + #o { background-color: #ff9900; } + #c { background-color: #46C7C7; } + #y { background-color: #FFFF00; } + .sel { background-color: #B9B9B9; } + .nsel { background-color: #E9E9E9; } + .c1 { background-color: #FFFBF2; } + .c2 { background-color: #FFF8CC; } + .c3 { background-color: #FAF0BE; } + .c4 { background-color: #F0EAD6; } + .c5 { background-color: #F3E5AB; } + .c6 { background-color: #F4C430; } + .c7 { background-color: #C2B280; color: white; } + .c8 { background-color: #DAA520; color: white; } + .c9 { background-color: #B8860B; color: white; } + .c10 { background-color: #918151; color: white; } + .c11 { background-color: #967117; color: white; } + .c12 { background-color: #6E5411; color: white; } + </style> + </head> + + <body> + <pre> + <span class=sel>Selected Sequences: 9 /Selected Residues: 174</span> + <span class=nsel>Deleted Sequences: 0 /Deleted Residues: 11</span> + + Gaps Scores: <span class=c1> =0= </span><span class=c2> <.001 </span><span class=c3> <.050 </span><span class=c4> <.100 </span><span class=c5> <.150 </span><span class=c6> <.200 </span><span class=c7> <.250 </span><span class=c8> <.350 </span><span class=c9> <.500 </span><span class=c10> <.750 </span><span class=c11> <1.00 </span><span class=c12> =1= </span> + + 10 20 30 40 50 60 70 80 90 100 110 120 + =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+ + <span class=sel>Csa004271</span> ---------------------------------M<span id=c>Y</span>M<span id=b>A</span><span id=b>M</span><span id=o>G</span><span id=c>H</span><span id=b>F</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span>KN<span id=b>I</span>SE<span id=c>Y</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>C<span id=g>S</span>E<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span>N<span id=r>K</span><span id=b>M</span><span id=b>I</span>E<span id=b>F</span>H<span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span>T<span id=g>T</span><span id=g>T</span><span id=c>Y</span>F<span id=y>P</span><span id=b>I</span><span id=r>K</span>A<span id=y>P</span><span id=o>G</span>SF<span id=m>D</span><span id=y>P</span>ANFNT<span id=b>I</span>K<span id=b>A</span><span id=b>M</span>N<span id=b>C</span><span id=b>A</span><span id=b>L</span>A<span id=b>L</span><span id=m>E</span>V<span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=r>K</span>S<span id=b>L</span><span id=b>L</span>A<span id=b>L</span> + <span class=sel>Xtr21234</span> ----MI<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span>SH<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>V</span><span id=g>N</span><span id=r>R</span>M<span id=b>V</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>M</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>S<span id=c>H</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=c>H</span>H<span id=b>V</span><span id=b>A</span>E<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>Q<span id=g>S</span>K<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>C</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>V</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span>T<span id=b>L</span><span id=m>D</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=g>T</span><span id=b>A</span><span id=b>L</span>D<span id=b>L</span><span id=m>E</span><span id=r>K</span>H<span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>LcaH</span> ----MS<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=b>F</span><span id=c>H</span>Q<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>Q<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span>V<span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>A<span id=c>Y</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span>Q<span id=b>A</span><span id=b>L</span><span id=c>H</span>N<span id=b>F</span><span id=b>A</span>K<span id=b>F</span><span id=b>F</span><span id=r>R</span>HQ<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>L</span><span id=g>Q</span><span id=g>N</span><span id=g>Q</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>V</span><span id=r>R</span><span id=r>K</span><span id=y>P</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>L</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span>S<span id=b>V</span><span id=g>N</span><span id=g>Q</span>S<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>Hsa167996</span> MTTAST<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>Q<span id=m>D</span>S<span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>Q<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span>V<span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>S<span id=c>Y</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span>KN<span id=b>F</span><span id=b>A</span>K<span id=c>Y</span><span id=b>F</span>LHQ<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>L</span><span id=g>Q</span><span id=g>N</span><span id=g>Q</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>D</span>C<span id=m>D</span><span id=m>D</span><span id=b>W</span>E--<span id=g>S</span><span id=o>G</span><span id=b>L</span>N<span id=b>A</span><span id=b>M</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=b>L</span>H<span id=b>L</span><span id=m>E</span><span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>S<span id=b>L</span><span id=b>L</span><span id=m>E</span><span id=b>L</span> + <span class=sel>Mmu024661</span> MTTAS<span id=y>P</span><span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>Q<span id=m>D</span><span id=b>A</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>Q<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span>V<span id=c>Y</span>L<span id=g>S</span><span id=b>M</span>S<span id=b>C</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span>KN<span id=b>F</span><span id=b>A</span>K<span id=c>Y</span><span id=b>F</span>LHQ<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>M</span>K<span id=b>L</span><span id=g>Q</span><span id=g>N</span><span id=g>Q</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>W</span>E--<span id=g>S</span><span id=o>G</span><span id=b>L</span>N<span id=b>A</span><span id=b>M</span><span id=m>E</span><span id=b>C</span><span id=b>A</span><span id=b>L</span>H<span id=b>L</span><span id=m>E</span><span id=r>K</span>S<span id=b>V</span><span id=g>N</span><span id=g>Q</span>S<span id=b>L</span><span id=b>L</span><span id=m>E</span><span id=b>L</span> + <span class=sel>Dre37936</span> ---MET<span id=g>S</span><span id=g>Q</span><span id=b>I</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=b>V</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>K</span>M<span id=b>I</span><span id=g>N</span><span id=b>L</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=o>G</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=c>H</span><span id=c>Y</span><span id=b>F</span>K<span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span><span id=b>A</span>K<span id=b>F</span><span id=b>F</span><span id=r>K</span>KN<span id=g>S</span>E<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>F</span><span id=b>M</span>E<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>V</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>D</span><span id=r>R</span><span id=m>D</span>V<span id=b>W</span><span id=o>G</span>--N<span id=o>G</span><span id=b>L</span>I<span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>LcaM</span> ----ME<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>V</span><span id=g>N</span><span id=r>R</span>M<span id=b>V</span><span id=g>N</span><span id=b>M</span><span id=m>E</span><span id=b>M</span><span id=b>F</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=b>F</span><span id=c>Y</span><span id=b>F</span>S<span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span>SH<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>N<span id=g>S</span>D<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>L</span>S<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span>H<span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span>K<span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>Tru14292</span> ----ME<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>K</span>M<span id=b>I</span><span id=g>N</span><span id=b>M</span><span id=m>E</span><span id=b>L</span><span id=c>Y</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=b>F</span><span id=b>F</span><span id=b>F</span>S<span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span><span id=b>A</span>H<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>N<span id=g>S</span>D<span id=m>E</span><span id=m>E</span><span id=r>R</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>E</span><span id=r>K</span><span id=b>L</span><span id=b>L</span>S<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span>K<span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + <span class=sel>Ola20972</span> ----ME<span id=g>S</span><span id=g>Q</span><span id=b>V</span><span id=r>R</span><span id=g>Q</span><span id=g>N</span><span id=c>Y</span><span id=c>H</span>R<span id=m>D</span><span id=b>C</span><span id=m>E</span><span id=b>A</span><span id=b>A</span><span id=b>I</span><span id=g>N</span><span id=r>R</span>M<span id=b>V</span><span id=g>N</span><span id=b>M</span><span id=m>E</span><span id=b>L</span><span id=b>F</span><span id=b>A</span><span id=g>S</span><span id=c>Y</span><span id=g>T</span><span id=c>Y</span>T<span id=g>S</span><span id=b>M</span>A<span id=b>F</span><span id=c>Y</span><span id=b>F</span><span id=m>D</span><span id=r>R</span><span id=m>D</span><span id=m>D</span><span id=b>V</span><span id=b>A</span><span id=b>L</span><span id=y>P</span><span id=o>G</span><span id=b>F</span>SH<span id=b>F</span><span id=b>F</span><span id=r>K</span><span id=m>E</span>N<span id=g>S</span>H<span id=m>E</span><span id=m>E</span><span id=r>K</span><span id=m>E</span><span id=c>H</span><span id=b>A</span><span id=m>D</span><span id=r>K</span><span id=b>L</span><span id=b>L</span>S<span id=b>F</span><span id=g>Q</span><span id=g>N</span><span id=r>K</span><span id=r>R</span><span id=o>G</span><span id=o>G</span><span id=r>R</span><span id=b>I</span><span id=b>F</span><span id=b>L</span><span id=g>Q</span><span id=m>D</span><span id=b>V</span><span id=r>K</span><span id=r>K</span><span id=y>P</span><span id=m>E</span><span id=r>R</span><span id=m>D</span><span id=m>E</span><span id=b>W</span><span id=o>G</span>--<span id=g>S</span><span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>A</span><span id=b>M</span><span id=g>Q</span><span id=b>C</span><span id=b>A</span><span id=b>L</span><span id=g>Q</span><span id=b>L</span><span id=m>E</span><span id=r>K</span><span id=g>N</span><span id=b>V</span><span id=g>N</span><span id=g>Q</span>A<span id=b>L</span><span id=b>L</span><span id=m>D</span><span id=b>L</span> + + Selected Cols: <span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span> + + Gaps Scores: <span class=c7> </span><span class=c7> </span><span class=c7> </span><span class=c8> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c5> </span><span class=c5> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span> + + 130 140 150 160 170 180 + =========+=========+=========+=========+=========+=========+===== + <span class=sel>Csa004271</span> <span id=c>H</span>E--<span id=g>T</span>AN<span id=o>G</span><span id=m>D</span><span id=y>P</span>E<span id=b>F</span>Q<span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span>AN<span id=b>F</span><span id=b>L</span>H<span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>D</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span>K<span id=m>D</span><span id=c>Y</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>KL<span id=b>V</span><span id=o>G</span>---T<span id=o>G</span><span id=b>L</span><span id=o>G</span><span id=m>E</span><span id=b>F</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span>FKSS----- + <span class=sel>Xtr21234</span> <span id=c>H</span>N<span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>E</span>RK<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>I</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>S</span>E<span id=c>H</span><span id=b>L</span><span id=m>D</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span>K<span id=c>H</span><span id=b>M</span><span id=r>K</span><span id=r>K</span><span id=b>F</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>K<span id=r>R</span><span id=b>L</span><span id=o>G</span><span id=b>V</span><span id=y>P</span>Q<span id=g>N</span><span id=o>G</span><span id=b>M</span><span id=o>G</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>S</span><span id=b>L</span>S------ + <span class=sel>LcaH</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>C</span><span id=g>S</span><span id=m>D</span><span id=c>H</span>N<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=m>D</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span>KS<span id=b>I</span><span id=r>K</span>E<span id=b>L</span>A<span id=m>D</span><span id=b>W</span><span id=b>V</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>R<span id=r>R</span><span id=b>M</span><span id=o>G</span><span id=b>A</span><span id=y>P</span>Q<span id=g>N</span><span id=o>G</span><span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>KES--S + <span class=sel>Hsa167996</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>D</span>KN<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span>K<span id=b>A</span><span id=b>I</span><span id=r>K</span>E<span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>V</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>R<span id=r>K</span><span id=b>M</span><span id=o>G</span><span id=b>A</span><span id=y>P</span>ES<span id=o>G</span><span id=b>L</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>DSDNES + <span class=sel>Mmu024661</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>D</span>KN<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>I</span><span id=m>E</span><span id=g>T</span><span id=c>Y</span><span id=c>Y</span><span id=b>L</span>S<span id=m>E</span><span id=g>Q</span><span id=b>V</span>KS<span id=b>I</span><span id=r>K</span>E<span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>V</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>R<span id=r>K</span><span id=b>M</span><span id=o>G</span><span id=b>A</span><span id=y>P</span>EA<span id=o>G</span><span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>H<span id=o>G</span>D-ES + <span class=sel>Dre37936</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>T</span><span id=m>E</span>M<span id=o>G</span><span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>S<span id=r>K</span><span id=b>M</span>D<span id=b>A</span><span id=o>G</span>N<span id=g>N</span>R<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span>DS----- + <span class=sel>LcaM</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>S</span><span id=m>D</span><span id=c>H</span><span id=o>G</span><span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>Y</span><span id=b>I</span><span id=g>S</span><span id=g>N</span><span id=b>L</span>S<span id=r>R</span><span id=b>M</span>D<span id=b>A</span>QK<span id=g>N</span>K<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>S</span><span id=b>L</span><span id=o>G</span><span id=o>G</span>KS--- + <span class=sel>Tru14292</span> <span id=c>H</span><span id=r>K</span><span id=b>L</span><span id=b>A</span><span id=g>S</span><span id=m>D</span><span id=c>H</span>V<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>L</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>S</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span><span id=b>A</span><span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>L</span><span id=o>G</span><span id=m>D</span><span id=c>Y</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>S<span id=r>R</span><span id=b>M</span>D<span id=b>A</span>QN<span id=g>N</span>K<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>SKS--- + <span class=sel>Ola20972</span> <span id=c>H</span><span id=r>K</span><span id=b>V</span><span id=b>A</span><span id=g>S</span><span id=m>D</span><span id=c>H</span>K<span id=m>D</span><span id=y>P</span><span id=c>H</span><span id=b>M</span><span id=b>C</span><span id=m>D</span><span id=b>F</span><span id=b>L</span><span id=m>E</span><span id=g>T</span><span id=c>H</span><span id=c>Y</span><span id=b>L</span><span id=g>N</span><span id=m>E</span><span id=g>Q</span><span id=b>V</span><span id=m>E</span>S<span id=b>I</span><span id=r>K</span><span id=r>K</span><span id=b>I</span><span id=o>G</span><span id=m>D</span><span id=c>H</span><span id=b>I</span><span id=g>T</span><span id=g>N</span><span id=b>L</span>T<span id=r>R</span><span id=b>M</span>D<span id=b>A</span><span id=c>H</span>T<span id=g>N</span>K<span id=b>M</span><span id=b>A</span><span id=m>E</span><span id=c>Y</span><span id=b>L</span><span id=b>F</span><span id=m>D</span><span id=r>K</span><span id=c>H</span><span id=g>T</span><span id=b>L</span><span id=o>G</span>SKS--- + + Selected Cols: <span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span> + + Gaps Scores: <span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c10> </span><span class=c10> </span><span class=c5> </span><span class=c7> </span><span class=c8> </span> + </pre> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmed_example.009.AA.mega Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,58 @@ +#MEGA +!Title ./test-data/example.009.AA.fasta; +!Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard; + +#Csa004271 +---------- ---------- ---------M YMAMGHFFDR DDVALKNISE +YFKECSEEER EHANKMIEFH NKRGGTTTYF PIKAPGSFDP ANTIKAMNCA +LALEVNVNKS LLALHE--TA NGDPEFQDFI EANFLHEQVD AIKKLKDYIT +NLKLVG---T GLGEFLFDKH FKSS + +#Xtr21234 +MISQVRQNYS HDCEAAVNRM VNLEMYASYT YLSMSHYFDR DDVALHHVAE +FFKEQSKEER ECAEKLMKCQ NKRGGRIVLQ DIKKPERDEW GSTLDAMQTA +LDLEKHVNQA LLDLHNLATE RKDPHICDFL ESEHLDEQVK HMKKFGDHIT +NLKRLGVPQN GMGEYLFDKH SLS- + +#LcaH +MSSQVRQNFH QDCEAAINRQ INLELYASYV YLSMAYYFDR DDQALHNFAK +FFRHQSHEER EHAEKLMKLQ NQRGGRIFLQ DVRKPDRDEW GSGVEALECA +LQLEKSVNQS LLDLHKLCSD HNDPHLCDFI ETHYLDEQVK SIKELADWVT +NLRRMGAPQN GMAEYLFDKH TLGK + +#Hsa167996 +STSQVRQNYH QDSEAAINRQ INLELYASYV YLSMSYYFDR DDVALKNFAK +YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDCDDW ESGLNAMECA +LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT +NLRKMGAPES GLAEYLFDKH TLGD + +#Mmu024661 +SPSQVRQNYH QDAEAAINRQ INLELYASYV YLSMSCYFDR DDVALKNFAK +YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDRDDW ESGLNAMECA +LHLEKSVNQS LLELHKLATD KNDPHLCDFI ETYYLSEQVK SIKELGDHVT +NLRKMGAPEA GMAEYLFDKH TLGH + +#Dre37936 +ETSQIRQNYV RDCEAAINKM INLELYAGYT YTSMAHYFKR DDVALPGFAK +FFKKNSEEER EHAEKFMEFQ NKRGGRIVLQ DIKKPDRDVW GNGLIAMQCA +LQLEKNVNQA LLDLHKLATE MGDPHLCDFL ETHYLNEQVE AIKKLGDHIT +NLSKMDAGNN RMAEYLFDKH TLDS + +#LcaM +MESQVRQNYH RDCEAAVNRM VNMEMFASYT YTSMAFYFSR DDVALPGFSH +FFKENSDEER EHAEKLLSFQ NKRGGHIFLQ DIKKPERDEW GSGLEAMQCA +LQLKKNVNQA LLDLHKLASD HGDPHLCDFL ETHYLNEQVE AIKKLGDYIS +NLSRMDAQKN KMAEYLFDKH SLGG + +#Tru14292 +MESQVRQNYH RDCEAAINKM INMELYASYT YTSMAFFFSR DDVALPGFAH +FFKENSDEER EHAEKLLSFQ NKRGGRIFLQ DIKKPERDEW GSGLEAMQCA +LQLEKKVNQA LLDLHKLASD HVDPHLCDFL ESHYLNEQVE AIKKLGDYIT +NLSRMDAQNN KMAEYLFDKH TLGS + +#Ola20972 +MESQVRQNYH RDCEAAINRM VNMELFASYT YTSMAFYFDR DDVALPGFSH +FFKENSHEEK EHADKLLSFQ NKRGGRIFLQ DVKKPERDEW GSGLEAMQCA +LQLEKNVNQA LLDLHKVASD HKDPHMCDFL ETHYLNEQVE SIKKIGDHIT +NLTRMDAHTN KMAEYLFDKH TLGS +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimal.xml Fri Nov 15 08:59:26 2024 +0000 @@ -0,0 +1,131 @@ +<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> + <description>for automated alignment trimming</description> + <macros> + <token name="@TOOL_VERSION@">1.5</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <xrefs> + <xref type="bio.tools">trimal</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">trimal</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + trimal -in '$in' -out '$trimmed_output' -htmlout '$html_summary' ${out_format_selector} + #if $trimming_mode.mode_selector == "custom" + -gapthreshold $trimming_mode.gapthreshold + -simthreshold $trimming_mode.simthreshold + -cons $trimming_mode.cons + #else: + $trimming_mode.mode_selector + #end if + + ]]></command> + <inputs> + <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" /> + <conditional name="trimming_mode"> + <param name="mode_selector" type="select" label="Select trimming mode from the list"> + <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option> + <option value="-noallgaps">noallgaps - remove columns composed only by gaps.</option> + <option value="-gappyout">gappyout - only uses information based on gaps' distribution.</option> + <option value="-strict">strict - combine gappyout trimming with subsequent trimming based on an automatically selected similarity threshold. </option> + <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option> + <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option> + <option value="custom">custom mode - eliminates a specified set of columns defined by the user.</option> + </param> + <when value="-nogaps" /> + <when value="-noallgaps"/> + <when value="-gappyout"/> + <when value="-strict"/> + <when value="-strictplus"/> + <when value="-automated1"/> + <when value="custom"> + <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Gap threshold" help="1 - (fraction of sequences with a gap allowed)."/> + <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/> + <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="Minimum conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve."/> + </when> + </conditional> + <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list"> + <option value="-clustal">CLUSTAL format</option> + <option value="-fasta">FASTA format</option> + <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option> + <option value="-nbrf">NBRF/PIR format</option> + <option value="-nexus">NEXUS format</option> + <option value="-mega">MEGA format</option> + <option value="-phylip">PHYLIP/PHYLIP4 format</option> + <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option> + <option value="-phylip_paml">PHYLIP format compatible with PAML</option> + <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option> + <option value="-phylip3.2">PHYLIP3.2 format</option> + <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option> + </param> + </inputs> + <outputs> + <data name="trimmed_output" format="fasta" label="Trimmed alignment."> + <change_format> + <when input="out_format_selector" value="-fasta" format="fasta" /> + <when input="out_format_selector" value="-fasta_m10" format="fasta" /> + <when input="out_format_selector" value="-phylip" format="phylip" /> + <when input="out_format_selector" value="-phylip_m10" format="phylip" /> + <when input="out_format_selector" value="-phylip_paml" format="phylip" /> + <when input="out_format_selector" value="-phylip_paml_m10" format="phylip" /> + <when input="out_format_selector" value="-phylip3.2" format="phylip" /> + <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" /> + <when input="out_format_selector" value="-clustal" format="clustal" /> + <when input="out_format_selector" value="-mega" format="mega" /> + <when input="out_format_selector" value="-nbrf" format="pir" /> + <when input="out_format_selector" value="-nexus" format="nexus" /> + </change_format> + </data> + <data name="html_summary" format="html" label="trimal html summary."/> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="in" value="example.009.AA.fasta"/> + <param name="mode_selector" value="-gappyout" /> + <param name="out_format_selector" value="-mega" /> + <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/> + <output name="html_summary" file="trimmed_example.009.AA.html"/> + </test> + <test expect_num_outputs="2"> + <param name="in" value="example.009.AA.fasta"/> + <param name="mode_selector" value="custom" /> + <param name="gapthreshold" value="0.5" /> + <param name="simthreshold" value="0.5" /> + <param name="cons" value="5" /> + <param name="out_format_selector" value="-phylip_paml_m10" /> + <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/> + <output name="html_summary" file="custom_trimmed_example.009.AA.html"/> + </test> + </tests> + <help><![CDATA[ + +TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. + +TrimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. +These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, +the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment. + +TrimAl implements a series of automated algorithms that trim the alignment searching for optimum thresholds based on inherent characteristics +of the input alignment, to be used so that the signal-to-noise ratio after alignment trimming phase is increased. Learn more about the available trimming modes here: https://trimal.readthedocs.io/en/latest/algorithms.html + +Among trimAl's additional features, trimAl allows: + +- getting the complementary alignment (columns that were trimmed), +- to compute statistics from the alignment, +- to select the output file format, +- to get a summary of trimAl's trimming in HTML and SVG formats, +- and many other options. + +TrimAl webpage: https://trimal.readthedocs.io + +License +------- +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, the last available version. + ]]></help> + <citations> + <citation type="doi">doi:10.1093/bioinformatics/btp348</citation> + </citations> +</tool> \ No newline at end of file