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annotate alignment/mafft.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 my $strategy = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $input = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $output = "seqs_aligned.fasta";
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6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 if($strategy eq "Auto") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 my $run = qx/mafft --auto $input > $output 2>log.txt/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 elsif($strategy eq "FFT-NS-1") {
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11 my $run = qx/mafft --retree 1 $input > $output 2>log.txt/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 elsif($strategy eq "FFT-NS-2") {
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14 my $run = qx/mafft --retree 2 $input > $output 2>log.txt/;
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15 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 elsif($strategy eq "FFT-NS-i") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 my $run = qx/mafft-fftnsi $input > $output 2>log.txt/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 elsif($strategy eq "E-INS-i") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 my $run = qx/mafft-einsi $input > $output 2>log.txt/;
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21 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 elsif($strategy eq "L-INS-i") {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 my $run = qx/mafft-linsi $input > $output 2>log.txt/;
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24 }
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25 elsif($strategy eq "G-INS-i") {
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26 my $run = qx/mafft-ginsi $input > $output 2>log.txt/;
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27 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 elsif($strategy eq "Q-INS-i") {
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29 my $run = qx/mafft-qinsi $input > $output 2>log.txt/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 }
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31
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32 print $run;