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Bio::Tree::DistanceFactory.3pm
Langue: en
Version: 2009-02-27 (fedora - 05/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tree::DistanceFactory - Construct a tree using distance based methodsSYNOPSIS
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.
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AUTHOR - Jason Stajich
Email jason-at-bioperl.orgAPPENDIX
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.
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