Bio::Tree::DistanceFactoryBio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. | |
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Bio::Tree::DistanceFactory Ranking & Summary
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- License:
- Perl Artistic License
- Price:
- FREE
- Publisher Name:
- Jason Stajich
- Publisher web site:
- http://search.cpan.org/~birney/bioperl-1.4/Bio/PopGen/IO.pm
Bio::Tree::DistanceFactory Tags
Bio::Tree::DistanceFactory Description
Bio::Tree::DistanceFactory is a Perl module to construct a tree using distance based methods. 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. Requirements: · Perl
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