Mercurial > repos > iuc > trimal
changeset 2:e379c0202766 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_example.009.AA.nexus Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,37 @@ +#NEXUS +BEGIN DATA; + DIMENSIONS NTAX=9 NCHAR=63; +FORMAT DATATYPE=PROTEIN INTERLEAVE=yes GAP=-; +[Name: Csa004271 Len: 63] +[Name: Xtr21234 Len: 63] +[Name: LcaH Len: 63] +[Name: Hsa167996 Len: 63] +[Name: Mmu024661 Len: 63] +[Name: Dre37936 Len: 63] +[Name: LcaM Len: 63] +[Name: Tru14292 Len: 63] +[Name: Ola20972 Len: 63] + +MATRIX +Csa004271 ---------- ----YMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Xtr21234 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +LcaH SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Hsa167996 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Mmu024661 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Dre37936 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +LcaM SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Tru14292 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL +Ola20972 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL + +Csa004271 EQVKDNLELF DKH +Xtr21234 EQVKDNLELF DKH +LcaH EQVKDNLELF DKH +Hsa167996 EQVKDNLELF DKH +Mmu024661 EQVKDNLELF DKH +Dre37936 EQVKDNLELF DKH +LcaM EQVKDNLELF DKH +Tru14292 EQVKDNLELF DKH +Ola20972 EQVKDNLELF DKH + +; +END;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_window_example.005.AA.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>Sp8 +FPWNGLQIHMMGIII--------------------------------------------- +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/custom_trimmed_window_example.009.AA.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,54 @@ +<!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: 6 /Selected Residues: 60</span> + <span class=nsel>Deleted Sequences: 0 /Deleted Residues: 30</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 + =========+=========+=========+=========+=========+=========+=========+=========+=========+ + <span class=sel>Sp8</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------------------------------------- + <span class=sel>Sp17</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>------------------------------------------------------------ + <span class=sel>Sp10</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------- + <span class=sel>Sp26</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIII------------------------------ + <span class=sel>Sp33</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- + <span class=sel>Sp6</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII + + 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><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=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=nsel> </span> + + Gaps Scores: <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=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=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span> + Similarity Scores: <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=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=c10> </span><span class=c10> </span><span class=c9> </span><span class=c9> </span><span class=c8> </span><span class=c8> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span> + </pre> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.out.phy Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,9 @@ + 6 19 +Sp17 LIGFLLLWQGLDLNKMPVF +Sp10 V--IMLAWLGLEINMMVII +Sp8 Y-GIVLPWNGLQIHMMGII +Sp33 A-GLHMAWGGLEINKQAIL +Sp6 L-GIYLAWLGLEINMMAII +Sp26 L-GLFLAWLGLEINMMAQI + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.phy Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,8 @@ + 6 60 +Sp17 --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF +Sp10 ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII +Sp8 ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHMMGII +Sp33 -----------PTIL---NIA-GLHMETDI-N-FS--LAWF-----QAWGGLEINKQAIL +Sp6 ----------ASGAI---LTL-GIYLFTLC-AVIS--VSWY-----LAWLGLEINMMAII +Sp26 AAAAAAAA----ALL---TYL-GLFLGTDY-----EN---FAAAAANAWLGLEINMMAQI +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.report.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,54 @@ +<!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: 6 /Selected Residues: 19</span> + <span class=nsel>Deleted Sequences: 0 /Deleted Residues: 41</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 + =========+=========+=========+=========+=========+=========+ + <span class=sel>Sp17</span> --------FAYTA<span id=y>P</span>D---L<span id=b>L</span><span id=b>L</span>I<span id=o>G</span><span id=b>F</span><span id=b>L</span><span id=b>L</span>K<span id=g>T</span>V<span id=b>A</span>-T-<span id=b>F</span><span id=o>G</span>--DT<span id=b>W</span><span id=b>F</span>-----Q<span id=b>L</span><span id=b>W</span>Q<span id=o>G</span><span id=b>L</span><span id=m>D</span><span id=b>L</span><span id=g>N</span>K<span id=b>M</span><span id=y>P</span><span id=b>V</span><span id=b>F</span> + <span class=sel>Sp10</span> ----------D<span id=y>P</span>A<span id=b>V</span><span id=b>L</span>----<span id=b>F</span><span id=b>V</span>--<span id=b>I</span><span id=b>M</span><span id=b>L</span><span id=o>G</span><span id=g>T</span>I<span id=g>T</span>-K-<span id=b>F</span><span id=g>S</span>--SE<span id=b>W</span><span id=b>F</span>-----F<span id=b>A</span><span id=b>W</span>L<span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>I</span><span id=g>N</span><span id=b>M</span><span id=b>M</span><span id=b>V</span><span id=b>I</span><span id=b>I</span> + <span class=sel>Sp8</span> ----------<span id=o>G</span>L<span id=o>G</span>K<span id=b>V</span>---I<span id=b>V</span><span id=c>Y</span>-<span id=o>G</span><span id=b>I</span><span id=b>V</span><span id=b>L</span><span id=o>G</span><span id=g>T</span>KS-DQ<span id=b>F</span><span id=g>S</span>NWVV<span id=b>W</span><span id=b>L</span>-----F<span id=y>P</span><span id=b>W</span>N<span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span>H<span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span> + <span class=sel>Sp33</span> -----------<span id=y>P</span>T<span id=b>I</span><span id=b>L</span>---N<span id=b>I</span><span id=b>A</span>-<span id=o>G</span><span id=b>L</span><span id=c>H</span><span id=b>M</span>E<span id=g>T</span>D<span id=b>I</span>-N-<span id=b>F</span><span id=g>S</span>--LA<span id=b>W</span><span id=b>F</span>-----Q<span id=b>A</span><span id=b>W</span><span id=o>G</span><span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>I</span><span id=g>N</span>KQ<span id=b>A</span><span id=b>I</span><span id=b>L</span> + <span class=sel>Sp6</span> ----------AS<span id=o>G</span><span id=b>A</span><span id=b>I</span>---L<span id=g>T</span><span id=b>L</span>-<span id=o>G</span><span id=b>I</span><span id=c>Y</span><span id=b>L</span>F<span id=g>T</span>L<span id=b>C</span>-AV<span id=b>I</span><span id=g>S</span>--VS<span id=b>W</span><span id=c>Y</span>-----L<span id=b>A</span><span id=b>W</span>L<span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>I</span><span id=g>N</span><span id=b>M</span><span id=b>M</span><span id=b>A</span><span id=b>I</span><span id=b>I</span> + <span class=sel>Sp26</span> AAAAAAAA----A<span id=b>L</span><span id=b>L</span>---T<span id=c>Y</span><span id=b>L</span>-<span id=o>G</span><span id=b>L</span><span id=b>F</span><span id=b>L</span><span id=o>G</span><span id=g>T</span>D<span id=c>Y</span>-----EN---<span id=b>F</span>AAAAAN<span id=b>A</span><span id=b>W</span>L<span id=o>G</span><span id=b>L</span><span id=m>E</span><span id=b>I</span><span id=g>N</span><span id=b>M</span><span id=b>M</span><span id=b>A</span>Q<span id=b>I</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=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=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=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=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=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=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c10> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c11> </span><span class=c12> </span><span class=c12> </span><span class=c6> </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=c1> </span><span class=c11> </span><span class=c8> </span><span class=c11> </span><span class=c11> </span><span class=c8> </span><span class=c8> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c12> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </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=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c2> </span><span class=c4> </span><span class=c5> </span><span class=c4> </span><span class=c5> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c4> </span><span class=c4> </span><span class=c5> </span><span class=c1> </span><span class=c12> </span><span class=c6> </span><span class=c4> </span><span class=c8> </span><span class=c4> </span><span class=c12> </span><span class=c3> </span><span class=c3> </span><span class=c1> </span><span class=c4> </span><span class=c2> </span><span class=c7> </span><span class=c7> </span><span class=c5> </span><span class=c2> </span><span class=c4> </span><span class=c4> </span><span class=c12> </span><span class=c6> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c3> </span><span class=c5> </span><span class=c12> </span><span class=c3> </span><span class=c12> </span><span class=c12> </span><span class=c7> </span><span class=c8> </span><span class=c7> </span><span class=c5> </span><span class=c7> </span><span class=c5> </span><span class=c6> </span><span class=c6> </span> + </pre> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.002.AA.stats.txt Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,216 @@ +| Residue % Gaps Gap Score | +| Number | ++----------------------------------------------+ + 0 83.33333333 0.1666666667 + 1 83.33333333 0.1666666667 + 2 83.33333333 0.1666666667 + 3 83.33333333 0.1666666667 + 4 83.33333333 0.1666666667 + 5 83.33333333 0.1666666667 + 6 83.33333333 0.1666666667 + 7 83.33333333 0.1666666667 + 8 83.33333333 0.1666666667 + 9 83.33333333 0.1666666667 + 10 33.33333333 0.6666666667 + 11 16.66666667 0.8333333333 + 12 0 1 + 13 0 1 + 14 0 1 + 15 100 0 + 16 100 0 + 17 100 0 + 18 16.66666667 0.8333333333 + 19 0 1 + 20 0 1 + 21 83.33333333 0.1666666667 + 22 16.66666667 0.8333333333 + 23 0 1 + 24 0 1 + 25 0 1 + 26 0 1 + 27 0 1 + 28 0 1 + 29 0 1 + 30 100 0 + 31 16.66666667 0.8333333333 + 32 66.66666667 0.3333333333 + 33 16.66666667 0.8333333333 + 34 16.66666667 0.8333333333 + 35 66.66666667 0.3333333333 + 36 66.66666667 0.3333333333 + 37 16.66666667 0.8333333333 + 38 16.66666667 0.8333333333 + 39 16.66666667 0.8333333333 + 40 0 1 + 41 83.33333333 0.1666666667 + 42 83.33333333 0.1666666667 + 43 83.33333333 0.1666666667 + 44 83.33333333 0.1666666667 + 45 83.33333333 0.1666666667 + 46 0 1 + 47 0 1 + 48 0 1 + 49 0 1 + 50 0 1 + 51 0 1 + 52 0 1 + 53 0 1 + 54 0 1 + 55 0 1 + 56 0 1 + 57 0 1 + 58 0 1 + 59 0 1 + +| Number of | Cumulative % Cumulative | Number of Gaps % Gaps Gap Score | +| Residues % Length | NumberResid. Length | per Column per Column per Column | ++-------------------------------+---------------------------------------+--------------------------------------------------+ + 27 45 27 45 0 0 1 + 9 15 36 60 1 0.1666666667 0.8333333333 + 1 1.666666667 37 61.66666667 2 0.3333333333 0.6666666667 + 3 5 40 66.66666667 4 0.6666666667 0.3333333333 + 16 26.66666667 56 93.33333333 5 0.8333333333 0.1666666667 + 4 6.666666667 60 100 6 1 0 + +| Residue Similarity | +| Number Value | ++----------------------------+ + 0 0 + 1 0 + 2 0 + 3 0 + 4 0 + 5 0 + 6 0 + 7 0 + 8 0 + 9 0 + 10 5.53110965e-07 + 11 1.646922465e-05 + 12 0.0006768687163 + 13 1.008950312e-05 + 14 0.0002165469632 + 15 0 + 16 0 + 17 0 + 18 2.547356235e-05 + 19 3.554812429e-05 + 20 0.000239324916 + 21 0 + 22 1 + 23 0.004173502792 + 24 1.045452791e-05 + 25 0.17306979 + 26 1.390550642e-05 + 27 1 + 28 4.909260952e-06 + 29 4.015034392e-06 + 30 0 + 31 3.165722228e-05 + 32 4.141910495e-07 + 33 0.01769078523 + 34 0.01232499164 + 35 0.0001380086615 + 36 5.576576978e-10 + 37 1.25446204e-05 + 38 5.194381811e-05 + 39 1 + 40 0.004842269234 + 41 0 + 42 0 + 43 0 + 44 0 + 45 0 + 46 2.948553856e-06 + 47 0.0006762341363 + 48 1 + 49 5.273301213e-06 + 50 1 + 51 1 + 52 0.01518695708 + 53 0.2151376605 + 54 0.02632254921 + 55 0.0008615002735 + 56 0.0174868498 + 57 0.000106244057 + 58 0.001373802545 + 59 0.007171744481 + +| Number of | Cumulative % Cumulative | Similarity | +| Residues % Length | NumberResid. Length | Value | ++-------------------------------+---------------------------------------+----------------+ + 6 10.00000015 6 10.00000015 1 + 1 1.666666754 7 11.66666672 0.2151376605 + 1 1.666666754 8 13.33333403 0.17306979 + 1 1.666666754 9 15.0000006 0.02632254921 + 1 1.666666754 10 16.66666716 0.01769078523 + 1 1.666666754 11 18.33333373 0.0174868498 + 1 1.666666754 12 20.0000003 0.01518695708 + 1 1.666666754 13 21.66666687 0.01232499164 + 1 1.666666754 14 23.33333343 0.007171744481 + 1 1.666666754 15 25 0.004842269234 + 1 1.666666754 16 26.66666806 0.004173502792 + 1 1.666666754 17 28.33333313 0.001373802545 + 1 1.666666754 18 30.00000119 0.0008615002735 + 1 1.666666754 19 31.66666627 0.0006768687163 + 1 1.666666754 20 33.33333433 0.0006762341363 + 1 1.666666754 21 34.9999994 0.000239324916 + 1 1.666666754 22 36.66666746 0.0002165469632 + 1 1.666666754 23 38.33333254 0.0001380086615 + 1 1.666666754 24 40.0000006 0.000106244057 + 1 1.666666754 25 41.66666567 5.194381811e-05 + 1 1.666666754 26 43.33333373 3.554812429e-05 + 1 1.666666754 27 44.99999881 3.165722228e-05 + 1 1.666666754 28 46.66666687 2.547356235e-05 + 1 1.666666754 29 48.33333194 1.646922465e-05 + 1 1.666666754 30 50 1.390550642e-05 + 1 1.666666754 31 51.66666508 1.25446204e-05 + 1 1.666666754 32 53.33333611 1.045452791e-05 + 1 1.666666754 33 55.00000119 1.008950312e-05 + 1 1.666666754 34 56.66666627 5.273301213e-06 + 1 1.666666754 35 58.33333135 4.909260952e-06 + 1 1.666666754 36 60.00000238 4.015034392e-06 + 1 1.666666754 37 61.66666746 2.948553856e-06 + 1 1.666666754 38 63.33333254 5.53110965e-07 + 1 1.666666754 39 64.99999762 4.141910495e-07 + 1 1.666666754 40 66.66666865 5.576576978e-10 + 20 33.33333433 60 100 0 + +## MaxIdentity 0.4474 +#> MaxIdentity Get the maximum identity value for any pair of sequences in the alignment + +## AverageIdentity 0.3056 +#> AverageIdentity Average identity between all sequences + +## Identity sequences matrix +Sp17 1.0000 0.2750 0.2093 0.2750 0.2683 0.2000 +Sp10 0.2750 1.0000 0.4000 0.4054 0.4474 0.3269 +Sp8 0.2093 0.4000 1.0000 0.2500 0.4000 0.2075 +Sp33 0.2750 0.4054 0.2500 1.0000 0.3421 0.2745 +Sp6 0.2683 0.4474 0.4000 0.3421 1.0000 0.3019 +Sp26 0.2000 0.3269 0.2075 0.2745 0.3019 1.0000 + +## AverageMostSimilarIdentity 0.3837 +#> AverageMostSimilarIdentity Average identity between most similar pair-wise sequences + +## Identity for most similar pair-wise sequences matrix +Sp17 0.2750 Sp10 +Sp10 0.4474 Sp6 +Sp8 0.4000 Sp10 +Sp33 0.4054 Sp10 +Sp6 0.4474 Sp10 +Sp26 0.3269 Sp10 + +## MaxOverlap 1.0000 +#> MaxOverlap Get the maximum overlap value for any pair of sequences in the alignment + +## AverageOverlap 0.8723 +#> AverageOverlap Average overlap between all sequences + +## Overlap sequences matrix +Sp17 1.0000 0.8750 0.9250 0.9000 0.9250 0.7250 +Sp10 1.0000 1.0000 1.0000 0.9714 1.0000 0.7714 +Sp8 0.9250 0.8750 1.0000 0.9000 0.9500 0.7750 +Sp33 1.0000 0.9444 1.0000 1.0000 1.0000 0.8056 +Sp6 0.9737 0.9211 1.0000 0.9474 1.0000 0.7632 +Sp26 0.6591 0.6136 0.7045 0.6591 0.6591 1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,24 @@ +>Sp8 +FPWNGLQIHMMGIII--------------------------------------------- +------------------------------ + +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +------------------------------ + +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +------------------------------ + +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +------------------------------ + +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +IIIIIIIIIIIIIII--------------- + +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +IIIIIIIIIIIIIIIIIIIIIIIIIIIIII +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.out.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>Sp8 +FPWNGLQIHMMGIII--------------------------------------------- +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.out.gappyout.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>Sp8 +FPWNGLQIHMMGIII--------------- +>Sp17 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp10 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp26 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp33 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII +>Sp6 +FPWNGLQIHMMGIIIIIIIIIIIIIIIIII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.out.overlaptrim.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,12 @@ +>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.005.AA.out.phylip Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,9 @@ + 6 60 +Sp8 FPWNGLQIHMMGIII--------------------------------------------- +Sp17 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------ +Sp10 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- +Sp26 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +Sp33 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +Sp6 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.report.gappyout.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,52 @@ +<!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: 6 /Selected Residues: 30</span> + <span class=nsel>Deleted Sequences: 0 /Deleted Residues: 60</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 + =========+=========+=========+=========+=========+=========+=========+=========+=========+ + <span class=sel>Sp8</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------------------------------------- + <span class=sel>Sp17</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>------------------------------------------------------------ + <span class=sel>Sp10</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------- + <span class=sel>Sp26</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIII------------------------------ + <span class=sel>Sp33</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- + <span class=sel>Sp6</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII + + 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=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=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=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=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=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> + + Gaps Scores: <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=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=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span> + </pre> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.report.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,52 @@ +<!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: 6 /Selected Residues: 60</span> + <span class=nsel>Deleted Sequences: 0 /Deleted Residues: 30</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 + =========+=========+=========+=========+=========+=========+=========+=========+=========+ + <span class=sel>Sp8</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------------------------------------- + <span class=sel>Sp17</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>------------------------------------------------------------ + <span class=sel>Sp10</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------- + <span class=sel>Sp26</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIII------------------------------ + <span class=sel>Sp33</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- + <span class=sel>Sp6</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII + + 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><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=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=nsel> </span> + + Gaps Scores: <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=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=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span> + </pre> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.005.AA.report.overlaptrim.html Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,52 @@ +<!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: 6 /Selected Residues: 15</span> + <span class=nsel>Deleted Sequences: 0 /Deleted Residues: 75</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 + =========+=========+=========+=========+=========+=========+=========+=========+=========+ + <span class=sel>Sp8</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------------------------------------- + <span class=sel>Sp17</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>------------------------------------------------------------ + <span class=sel>Sp10</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>--------------------------------------------- + <span class=sel>Sp26</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIII------------------------------ + <span class=sel>Sp33</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIII--------------- + <span class=sel>Sp6</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII + + 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=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=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=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=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=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=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=nsel> </span><span class=nsel> </span><span class=nsel> </span> + + Gaps Scores: <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=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=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span> + </pre> + </body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example.009.AA.out.notrim.fasta Wed Nov 20 22:30:36 2024 +0000 @@ -0,0 +1,16 @@ +>Csa004271 +----------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEERE +HANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLALHE--T +ANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS---- +>LcaH +---SSQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQSHEERE +HAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDLHKLCS +DHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGKES-S +>Mmu024661 +MTAPSQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEERE +HAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLELHKLAT +DKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGHGDES +>Ola20972 +---ESQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENSHEEKE +HADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDLHKVAS +DHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS--
--- a/test-data/trimmed_example.009.AA.mega Mon Nov 18 07:06:34 2024 +0000 +++ b/test-data/trimmed_example.009.AA.mega Wed Nov 20 22:30:36 2024 +0000 @@ -1,5 +1,5 @@ #MEGA -!Title ./test-data/example.009.AA.fasta; +!Title /tmp/saskia/tmpk459g5o_/files/1/8/2/dataset_182865f6-cd70-425d-9a26-7a7fa9974877.dat; !Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard; #Csa004271
--- a/trimal.xml Mon Nov 18 07:06:34 2024 +0000 +++ b/trimal.xml Wed Nov 20 22:30:36 2024 +0000 @@ -1,28 +1,82 @@ -<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> +<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT"> <description>for automated alignment trimming</description> <macros> <token name="@TOOL_VERSION@">1.5.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> + <edam_topics> + <edam_topic>topic_3293</edam_topic> <!-- phylogenetics --> + <edam_topic>topic_0080</edam_topic> <!-- sequence analysis --> + </edam_topics> + <edam_operations> + <edam_operation>operation_3192</edam_operation> <!--sequence trimming --> + </edam_operations> <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: - $trimming_mode.mode_selector - #end if + <command detect_errors="aggressive"><![CDATA[ + +trimal -in '$in' +-out '$trimmed_output' +${out_format_selector} + +#unless $trimming_mode.mode_selector == "manual" + -htmlout '$html_summary' +#end unless + +#if $trimming_mode.mode_selector == "custom" + -gapthreshold $trimming_mode.gapthreshold + -simthreshold $trimming_mode.simthreshold + -cons $trimming_mode.cons + + #if $trimming_mode.w + -w $trimming_mode.w + #else + #if $trimming_mode.gw + -gw $trimming_mode.gw + #end if + #if $trimming_mode.sw + -sw $trimming_mode.sw + #end if + #if $trimming_mode.cw + -cw $trimming_mode.cw + #end if + #end if +#else if $trimming_mode.mode_selector == "manual" + #if $trimming_mode.selectcols + -selectcols { $trimming_mode.selectcols } + #end if + #if $trimming_mode.selectseqs + -selectseqs { $trimming_mode.selectseqs } + #end if +#else + $trimming_mode.mode_selector +#end if + +#if $resoverlap + -resoverlap $resoverlap +#end if +#if $seqoverlap + -seqoverlap $seqoverlap +#end if + +#if $statistics +-sgc +-sgt +-ssc +-sst +-sident +-soverlap +| tee '$statsout' +#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)" /> + <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" 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> @@ -31,7 +85,8 @@ <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> + <option value="custom">custom mode - define trimming parameters yourself.</option> + <option value="manual">manual mode - specify columns or sequences to remove</option> </param> <when value="-nogaps" /> <when value="-noallgaps"/> @@ -39,13 +94,35 @@ <when value="-strict"/> <when value="-strictplus"/> <when value="-automated1"/> + <when value="manual"> + <param argument="-selectcols" type="text" optional="true" label="Columns to be removed from alignment" help="Example: '2,4,8-12'; Range: [0 - (Number of Columns - 1)]"> + <validator type="regex" message="must be comma-separated list of whole numbers">(\d+)([,-]\d+)*</validator> + </param> + <param argument="-selectseqs" type="text" optional="true" label="Sequences to be removed from alignment" help="Example: '2,4,8-12'; Range: [0 - (Number of Sequences - 1)]"> + <validator type="regex" message="must be comma-separated list of whole numbers">(\d+)([,-]\d+)*</validator> + </param> + </when> <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="-conthreshold" type="float" optional="true" min="0" max="100" label="Consistency Threshold. Minimum consistency value required" help="Range: [0 - 1]. Not allowed in combination with inputfile."/> <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."/> + <param argument="-clusters" type="integer" optional="true" min="0" label="Clusters. Get the most Nth representatives sequences from a given alignment." help="Range: [1 - (Number of sequences)]"/> + <param argument="-maxidentity" type="float" optional="true" min="0" max="1" label="Max Identity. Get the representatives sequences for a given identity threshold. " help="Range: [0 - 1]"/> + + <param argument="-w" type="integer" optional="true" min="0" label="Window frame size - general" help="score of position i is the average of the window (i - n) to (i + n). Will override specific sizes set below"/> + <param argument="-gw" type="integer" optional="true" min="0" label="Window frame size applied to Gaps" help="score of position i is the average of the window (i - n) to (i + n)."/> + <param argument="-sw" type="integer" optional="true" min="0" label="Window frame size applied to Similarity" help="score of position i is the average of the window (i - n) to (i + n)."/> + <param argument="-cw" type="integer" optional="true" min="0" label="Window frame size applied to Consistency" help="score of position i is the average of the window (i - n) to (i + n)."/> + + </when> </conditional> + <param argument="-resoverlap" type="float" optional="true" min="0" max="1" label="Residue overlap" help="Minimum overlap of a positions with other positions in the column to be considered a “good position”. Range: [0-1]. Must be used in combination with Sequence overlap."/> + <param argument="-seqoverlap" type="integer" optional="true" min="0" max="100" label="Sequence overlap" help="Minimum percentage of “good positions” that a sequence must have in order to be conserved. Range: [0-100]. Must be used in combination with Residue overlap."/> + <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list"> + <option value="" selected="true">Same as input (default)</option> <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> @@ -59,9 +136,10 @@ <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> + <param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/> </inputs> <outputs> - <data name="trimmed_output" format="fasta" label="Trimmed alignment."> + <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment."> <change_format> <when input="out_format_selector" value="-fasta" format="fasta" /> <when input="out_format_selector" value="-fasta_m10" format="fasta" /> @@ -77,17 +155,22 @@ <when input="out_format_selector" value="-nexus" format="nexus" /> </change_format> </data> - <data name="html_summary" format="html" label="trimal html summary."/> + <data name="html_summary" format="html" label="${tool.name} on ${on_string}: HTML report"> + <filter> trimming_mode['mode_selector'] != 'manual' </filter> + </data> + <data name="statsout" format="txt" label="${tool.name} on ${on_string}: statistics"> + <filter> statistics </filter> + </data> </outputs> <tests> - <test expect_num_outputs="2"> + <test expect_num_outputs="2"><!-- test automated trim setting --> <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"/> + <output name="trimmed_output" file="trimmed_example.009.AA.mega" ftype="mega" lines_diff="2"/> + <output name="html_summary" file="trimmed_example.009.AA.html" ftype="html"/> </test> - <test expect_num_outputs="2"> + <test expect_num_outputs="2"><!-- test custom trim setting --> <param name="in" value="example.009.AA.fasta"/> <param name="mode_selector" value="custom" /> <param name="gapthreshold" value="0.5" /> @@ -95,7 +178,55 @@ <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"/> + <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/> + </test> + <test expect_num_outputs="2"><!-- test additionalcustom trim setting --> + <param name="in" value="example.009.AA.fasta"/> + <param name="mode_selector" value="custom" /> + <param name="gapthreshold" value="0.75" /> + <param name="simthreshold" value="0.8" /> + <param name="cons" value="5" /> + <param name="conthreshold" value="0.5" /> + <param name="clusters" value="4" /> + <param name="maxidentity" value="0.8" /> + <param name="out_format_selector" value="-nexus" /> + <output name="trimmed_output" file="custom_trimmed_example.009.AA.nexus" ftype="nexus"/> + <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/> + </test> + <test expect_num_outputs="2"><!-- test window settings --> + <param name="in" value="example.005.AA.fasta"/> + <param name="mode_selector" value="custom" /> + <param name="gapthreshold" value="0.5" /> + <param name="simthreshold" value="0.5" /> + <param name="conthreshold" value="0.5" /> + <param name="gw" value="3"/> + <param name="sw" value="4"/> + <param name="cw" value="5"/> + <output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/> + <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html"/> + </test> + <test expect_num_outputs="3"><!-- test with phylip input and output statistics --> + <param name="in" value="example.002.AA.phy" ftype="phylip"/> + <param name="mode_selector" value="-strict"/> + <param name="statistics" value="true"/> + <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip" lines_diff="0"/> + <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="0"/> + <output name="statsout" file="example.002.AA.stats.txt" ftype="txt" lines_diff="0"/> + </test> + <test expect_num_outputs="2"><!-- test with overlap trimming --> + <param name="in" value="example.005.AA.fasta" ftype="fasta"/> + <param name="mode_selector" value="-nogaps"/> + <param name="resoverlap" value="0.8"/> + <param name="seqoverlap" value="6"/> + <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta" lines_diff="0"/> + <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="0"/> + </test> + <test expect_num_outputs="1"><!-- test with manual trimming --> + <param name="in" value="example.009.AA.fasta" ftype="fasta"/> + <param name="mode_selector" value="manual"/> + <param name="selectcols" value="2,4,7-9"/> + <param name="selectseqs" value="1,3,5-7"/> + <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta" lines_diff="0"/> </test> </tests> <help><![CDATA[ @@ -113,19 +244,19 @@ - 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, +- 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 +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 +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> + <citation type="doi">10.1093/bioinformatics/btp348</citation> </citations> -</tool> \ No newline at end of file +</tool>