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.