examples/tree/paup2phylip.pl

   1 #!/usr/bin/perl
   2 # Author: Jason Stajich <jason.stajich@duke.edu>
   3 # Convert a PAUP tree block to Phylip format
   4
   5 use strict;
   6
   7 my @data;
   8 while(<>) {
   9     last if( /Translate/ );
  10 }
  11 while(<>) {
  12     last if (/;/);
  13     my ($num, $taxon) = (/\s+(\d+)\s([A-Za-z\.\_]+),/);
  14     $data[$num] = substr($taxon,0,10);
  15 }
  16 while(<>) {
  17     next unless (s/^\s*tree (\S+) = \[\S+\] //i);
  18     my $tree = $_;
  19     for( my $i=scalar @data; $i > 0; $i-- ) {
  20         my $taxon = $data[$i];
  21         $tree =~ s/$i/$taxon/;
  22     }
  23     print $tree;
  24 }