| Bio::Tree::DistanceFactory(3pm) | User Contributed Perl Documentation | Bio::Tree::DistanceFactory(3pm) |
Bio::Tree::DistanceFactory - Construct a tree using distance based methods
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 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.
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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) Function: 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, 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.
| 2021-08-15 | perl v5.32.1 |