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://redmine.open-bio.org/projects/bioperl/

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.