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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:

	 http://bugzilla.open-bio.org/

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 v5.14.1			  2011-07-22	 Bio::Tree::DistanceFactory(3)
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