Bio::Tree::DistanceFactory 1.5.2_102

Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods.

SYNOPSIS

use Bio::Tree::DistanceFactory;
use Bio::AlignIO;
use Bio::Align::DNAStatistics;
my $tfactory = Bio::Tree::DistanceFactory->new(-method => "NJ");
my $stats = Bio::Align::DNAStatistics->new();

my $alnin = Bio::AlignIO->new(-format => clustalw,
-file => file.aln);
my $aln = $alnin->next_aln;
# Of course matrix can come from a different place
# like PHYLIP if you prefer, Bio::Matrix::IO should be able
# to parse many things
my $jcmatrix = $stats->distance(-align => $aln,
-method => Jukes-Cantor);
my $tree = $tfactory->make_tree($jcmatrix);

This is a factory which will construct a phylogenetic tree based on the pairwise sequence distances for a set of sequences. Currently UPGMA (Sokal and Michener 1958) and NJ (Saitou and Nei 1987) tree construction methods are implemented.