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

       Bio::Tree::DistanceFactory - Construct a	tree using distance based

	 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);

       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.

       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

       Saitou N	and Nei	M, (1987) "The neighbor-joining	method:	a new method
       for reconstructing phylogenetic trees." Mol Biol	Evol 4(4):406-25.

   Mailing Lists
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       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.

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       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:

AUTHOR - Jason Stajich

       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

	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'

	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

	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

	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

	Title	: method
	Usage	: $obj->method($newval)
	Example	:
	Returns	: value	of method (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

	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, 1999-12-07 version 0.3
		    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)


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