NAME

Bio::Phylo::Forest - Container for tree objects

SYNOPSIS

 use Bio::Phylo::Factory;
 my $fac = Bio::Phylo::Factory->new;
 my $forest = $fac->create_forest;
 my $tree = $fac->create_tree;
 $forest->insert($tree);
 print $forest->to_nexus;

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.

CALCULATIONS

calc_split_frequency()

Calculates frequency of provided split

 Type    : Calculation
 Title   : calc_split_frequency
 Usage   : my $freq = $trees->calc_split_frequency([$node1,$node2]);
 Function: Calculates split frequency
 Returns : Scalar, a number
 Args    : An array of taxon objects, or a taxa object
 Comment :

METHODS

insert()

Inserts trees in forest.

 Type    : Method
 Title   : insert
 Usage   : $trees->insert( $tree1, $tree2, ... );
 Function: Inserts trees in forest.
 Returns : A Bio::Phylo::Forest object.
 Args    : Trees
 Comment : The last seen tree that is set as default
           becomes the default for the entire forest

get_default_tree()

Gets the default tree in the forest.

 Type    : Method
 Title   : get_default_tree
 Usage   : my $tree = $trees->get_default_tree;
 Function: Gets the default tree in the forest.
 Returns : A Bio::Phylo::Forest::Tree object.
 Args    : None
 Comment : If no default tree has been set, 
           returns first tree. 

check_taxa()

Validates taxon links of nodes in invocant's trees.

 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

make_consensus()

Creates a consensus tree.

 Type    : Method
 Title   : make_consensus
 Usage   : my $tree = $obj->make_consensus
 Function: Creates a consensus tree
 Returns : $tree
 Args    : Optional:
           -fraction  => a fraction that specifies the cutoff frequency for including
                     bipartitions in the consensus. Default is 0.5 (MajRule)
           -branches  => 'frequency' or 'average', sets branch lengths to bipartition
                         frequency or average branch length in input trees
           -summarize => 'fraction' or 'probability', sets node label as either the
                         fraction of this bipartition on the whole (e.g. "85/100") or
                         as a probability (e.g. "0.85")

make_matrix()

Creates an MRP matrix object.

 Type    : Method
 Title   : make_matrix
 Usage   : my $matrix = $obj->make_matrix
 Function: Creates an MRP matrix object
 Returns : $matrix
 Args    : NONE

make_taxa()

Creates a taxa block from the objects contents if none exists yet.

 Type    : Method
 Title   : make_taxa
 Usage   : my $taxa = $obj->make_taxa
 Function: Creates a taxa block from the objects contents if none exists yet.
 Returns : $taxa
 Args    : NONE

to_newick()

Serializes invocant to newick string.

 Type    : Stringifier
 Title   : to_newick
 Usage   : my $string = $forest->to_newick;
 Function: Turns the invocant forest object 
           into a newick string, one line per tree
 Returns : SCALAR
 Args    : The same arguments as 
           Bio::Phylo::Forest::Tree::to_newick

to_nexus()

Serializer to nexus format.

 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 true)
           -make_translate => 1 (autogenerate translation table, overrides -translate => {})
                   
                   # when making a translation table, which index to start (default is
                   # 1, BayesTraits needs 0)
                   -translate_start => 1
 Comments:

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::Listable

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

Bio::Phylo::Taxa::TaxaLinker

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

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63