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Christopher Fields > BioPerl-1.6.924 > Bio::Tree::DistanceFactory



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Module Version: 1.006924   Source   Latest Release: BioPerl-1.007002


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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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.
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