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bio::tree::distancefactory(3pm) [debian man page]

Bio::Tree::DistanceFactory(3pm) 			User Contributed Perl Documentation			   Bio::Tree::DistanceFactory(3pm)

NAME
Bio::Tree::DistanceFactory - 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); DESCRIPTION
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. REFERENCES
Eddy SR, Durbin R, Krogh A, Mitchison G, (1998) "Biological Sequence Analysis", Cambridge Univ Press, Cambridge, UK. Howe K, Bateman A, Durbin R, (2002) "QuickTree: building huge Neighbour-Joining trees of protein sequences." Bioinformatics 18(11):1546-1547. Saitou N and Nei M, (1987) "The neighbor-joining method: a new method for reconstructing phylogenetic trees." Mol Biol Evol 4(4):406-25. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::Tree::DistanceFactory->new(); Function: Builds a new Bio::Tree::DistanceFactory object Returns : an instance of Bio::Tree::DistanceFactory Args : -method => 'NJ' or 'UPGMA' make_tree Title : make_tree Usage : my $tree = $disttreefact->make_tree($matrix); Function: Build a Tree based on a distance matrix Returns : L<Bio::Tree::TreeI> Args : L<Bio::Matrix::MatrixI> object _nj Title : _nj Usage : my $tree = $disttreefact->_nj($matrix); Function: Construct a tree based on distance matrix using the Neighbor Joining algorithm (Saitou and Nei, 1987) Implementation based on Kevin Howe's Quicktree implementation and uses his tricks (some based on Bill Bruno's work) to eliminate negative branch lengths Returns : L<Bio::Tree::TreeI> Args : L<Bio::Matrix::MatrixI> object _upgma Title : _upgma Usage : my $tree = $disttreefact->_upgma($matrix); Function: Construct a tree based on alignment using UPGMA Returns : L<Bio::Tree::TreeI> Args : L<Bio::Matrix::MatrixI> object method Title : method Usage : $obj->method($newval) Function: Example : Returns : value of method (a scalar) Args : on set, new value (a scalar or undef, optional) check_additivity Title : check_additivity Usage : if( $distance->check_additivity($matrix) ) { } Function : See if matrix obeys additivity principal Returns : boolean Args : Bio::Matrix::MatrixI References: Based on a Java implementation by Peter Sestoft, sestoft@dina.kvl.dk 1999-12-07 version 0.3 http://www.dina.kvl.dk/~sestoft/bsa.html which in turn is based on algorithms described in R. Durbin, S. Eddy, A. Krogh, G. Mitchison. Biological Sequence Analysis CUP 1998, Chapter 7. perl v5.14.2 2012-03-02 Bio::Tree::DistanceFactory(3pm)
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