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Bio::Tree::DistanceFactory 1.5.2_102

  Date Added: November 22, 2010  |  Visits: 614

Bio::Tree::DistanceFactory

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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: No special requirements
Platforms: Linux
Keyword: Based Biotreedistancefactory Construct Distance Distancefactory Libraries Perl Module Programming Tree Using
Users rating: 0/10

License: Freeware Size: 5.6 MB
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