/ 
BioPerl-1.7.8
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Tree::DistanceFactory

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://github.com/bioperl/bioperl-live/issues

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.