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

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $new_sequences = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 my $existing_alignment = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 my $output = "seqs_aligned.fasta";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 system "mafft --add $new_sequences --reorder $existing_alignment > $output 2>log.txt ";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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