NAME

Bio::Phylo::Forest - The forest object, a set of phylogenetic trees.

SYNOPSIS

use Bio::Phylo::Forest;
my $trees = Bio::Phylo::Forest->new;

DESCRIPTION

The Bio::Phylo::Forest object models a set of trees. The object subclasses the Bio::Phylo::Listable object, so look there for more methods available to forest objects.

METHODS

CONSTRUCTOR

new

Type    : Constructor
Title   : new
Usage   : my $trees = Bio::Phylo::Forest->new;
Function: Instantiates a Bio::Phylo::Forest object.
Returns : A Bio::Phylo::Forest object.
Args    : None required, though see the superclass
          Bio::Phylo::Listable from which this
          object inherits.

METHODS

check_taxa

Type    : Method
Title   : check_taxa
Usage   : $trees->check_taxa;
Function: Validates the taxon links of the
          nodes of the trees in $trees
Returns : A validated Bio::Phylo::Forest object.
Args    : None

to_nexus()

Type    : Format convertor
Title   : to_nexus
Usage   : my $data_block = $matrix->to_nexus;
Function: Converts matrix object into a nexus data block.
Returns : Nexus data block (SCALAR).
Args    : Trees can be formatted using the same arguments as those
		   passed to Bio::Phylo::Unparsers::Newick. In addition, you
		   can provide: 
		   
		   # as per mesquite's inter-block linking system (default is false):
		   -links => 1 (to create a TITLE token, and a LINK token, if applicable)
		   
		   # rooting is determined based on basal trichotomy. "token" means 'TREE' or 'UTREE'
		   # is used, "comment" means [&R] or [&U] is used, "nhx" means [%unrooted=on] or
		   # [%unrooted=off] if used, default is "comment"
		   -rooting => one of (token|comment|nhx)
		   
		   # to map taxon names to indices (default is false)
		   -make_translate => 1 (autogenerate translation table, overrides -translate => {})
Comments:

SEE ALSO

Bio::Phylo::Listable

The forest object inherits from the Bio::Phylo::Listable object. The methods defined therein are applicable to forest objects.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Forest.pm 4193 2007-07-11 20:26:06Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.