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Bio::Tree::DistanceFacUser(Contributed Perl DocumBio::Tree::DistanceFactory(3)

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.

perl v5.24.1			  2017-07-08	 Bio::Tree::DistanceFactory(3)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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