[Bioperl-l] bootstrap replicates

lberna at adinet.com.uy lberna at adinet.com.uy
Wed Apr 20 09:46:17 UTC 2011


Hi, I am new user of bioperl, 
I am trying to perform a phylogeny with replicate, but I do not 
understand how to use the bootsrap_replicate module.

this is my code, with out the boostrap, and works
#!/usr/bin/perl -w

use Bio::AlignIO;
use Bio::Align::DNAStatistics;
use Bio::Tree::DistanceFactory;
use Bio::TreeIO;
use Bio::Align::Utilities qw(:all);
# for a dna alignment
my $alnio = Bio::AlignIO->new(-file => $ARGV[0], -format=>'clustalw');
my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ');
my $stats = Bio::Align::DNAStatistics->new;
my $treeout = Bio::TreeIO->new(-format => 'newick');

while(my $aln = $alnio->next_aln ) {
my $mat = $stats->distance(-method => 'Kimura',
                            -align  => $aln);

my $tree = $dfactory->make_tree($mat);
$treeout->write_tree($tree);
}
print $treeout;
--------------------------------------------------------------------
but I want to incorporate the bootstrap, all form that I tried doesn't 
work... 

#use Bio::Align::Utilities qw(:all);
#my $replicates = bootstrap_replicates($aln,100);

Can somebody help me??
thanks a lot!
Luisa



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