[Bioperl-l] Cladogram construction

[Julian Onions]

Does anyone have any sample code for building cladograms based on Pars (one
of Phylip tools) type format (or any other format actually)
I've got something sort of working but I get no weights on the tree -
everything appears as nan. I'd also like to set one of the species to be an
outgroup. This is the closest sample I've found so far.


#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
use Bio::Tree::DistanceFactory;
use Bio::Align::ProteinStatistics;
use Bio::TreeIO;
use Bio::Tree::Draw::Cladogram;
my $alnfile = shift @ARGV || die "need a file to run";

my $input= Bio::AlignIO->new(-format => 'fasta',
    -file    => $alnfile);

if( my $aln = $input->next_aln ) {
 my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ');
 my $stats = Bio::Align::ProteinStatistics->new;
 my $distmat = $stats->distance(-align => $aln,
         -method => 'Kimura');
 my $treeout = Bio::TreeIO->new(-format => 'newick');
 my $tree = $dfactory->make_tree($distmat);
 $treeout->write_tree($tree);
  my $obj1 = Bio::Tree::Draw::Cladogram->new(-tree    => $tree,
                                             -compact => 0);
  $obj1->print(-file => "tree.eps");
} else {
 die "could not find any alignments in the file $alnfile";
}



Pars input looks like
3 4
Robin   101
Blackbird 100
Sparrow 100


Thanks,
Julian.