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#!/usr/bin/perl -w
use strict;
=head1 NAME
run_neighbor - run Phylip's 'neighbor' program through Bioperl
run_neighbor [-i inputfile] [-o outfilename]
Provide an matrix file to run neighbor on. File should be named of
the forma file.matrix or file.protdist (the ending doesn't matter, but
the program expects a file in the form of (\S+)\.(\S+).
This will run the application 'neighbor' to build a
Neighbor-Joining tree from a protein distance matrix.
=head1 AUTHOR
Jason Stajich, jason-AT-open-bio-DOT-org
use Bio::TreeIO;
use Bio::Tools::Run::Phylo::Phylip::Neighbor;
use Getopt::Long;
my @params = ('type'=>'NJ', 'quiet' => 1);
my $matrixfile;
my $out;
'i|input:s' => \$matrixfile,
'o|out:s' => \$out,
'h|help' => sub { exec('perldoc',$0); exit(0) }
($matrixfile) ||= shift @ARGV;
my ($stem,$ext) = ($matrixfile =~ /(\S+)\.(\S+)$/) ;
$stem ||= $matrixfile;
my $outfh;
if( $out ) {
open($outfh, ">$out") || die($!);
} else {
open($outfh, ">$stem.tree") || die($!);
my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
my (@trees) = $tree_factory->create_tree($matrixfile);
my $outtree = new Bio::TreeIO(-fh => $outfh);
foreach my $tree ( @trees ){
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