Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff alignment/mafft.pl @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alignment/mafft.pl Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,32 @@ +#!/usr/bin/perl + +my $strategy = $ARGV[0]; +my $input = $ARGV[1]; +my $output = "seqs_aligned.fasta"; + +if($strategy eq "Auto") { + my $run = qx/mafft --auto $input > $output 2>log.txt/; +} +elsif($strategy eq "FFT-NS-1") { + my $run = qx/mafft --retree 1 $input > $output 2>log.txt/; +} +elsif($strategy eq "FFT-NS-2") { + my $run = qx/mafft --retree 2 $input > $output 2>log.txt/; +} +elsif($strategy eq "FFT-NS-i") { + my $run = qx/mafft-fftnsi $input > $output 2>log.txt/; +} +elsif($strategy eq "E-INS-i") { + my $run = qx/mafft-einsi $input > $output 2>log.txt/; +} +elsif($strategy eq "L-INS-i") { + my $run = qx/mafft-linsi $input > $output 2>log.txt/; +} +elsif($strategy eq "G-INS-i") { + my $run = qx/mafft-ginsi $input > $output 2>log.txt/; +} +elsif($strategy eq "Q-INS-i") { + my $run = qx/mafft-qinsi $input > $output 2>log.txt/; +} + +print $run;