/ 
Bio-Phylo-0.49
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Forest

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.

METHODS

CONSTRUCTOR

new()

Forest constructor.

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.

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
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