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Bio-Phylo-0.17_RC1
River stage two • 9 direct dependents • 18 total dependents
8 ++
/ Bio::Phylo::Forest

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.