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Bio::Phylo::Forest::TrUser)Contributed Perl DocumenBio::Phylo::Forest::Tree(3)

NAME
       Bio::Phylo::Forest::Tree	- Phylogenetic tree

SYNOPSIS
	# some way to get a tree
	use Bio::Phylo::IO;
	my $string = '((A,B),C);';
	my $forest = Bio::Phylo::IO->parse(
	   -format => 'newick',
	   -string => $string
	);
	my $tree = $forest->first;

	# do something:
	print $tree->calc_imbalance;

	# prints "1"

DESCRIPTION
       The package has the getters and setters that alter the internal state
       of a tree object. Additional tree-related behaviours (which are
       available also) are defined in the package
       Bio::Phylo::Forest::TreeRole.

METHODS
   MUTATORS
       set_as_unrooted()
	   Sets	tree to	be interpreted as unrooted.

	    Type    : Mutator
	    Title   : set_as_unrooted
	    Usage   : $tree->set_as_unrooted;
	    Function: Sets tree	to be interpreted as unrooted.
	    Returns : $tree
	    Args    : NONE
	    Comments: This is a	flag to	indicate that the invocant
		      is interpreted to	be unrooted (regardless	of
		      topology). The object is otherwise unaltered,
		      this method is only here to capture things such
		      as the [&U] token	in nexus files.

       set_as_default()
	   Sets	tree to	be the default tree in a forest

	    Type    : Mutator
	    Title   : set_as_default
	    Usage   : $tree->set_as_default;
	    Function: Sets tree	to be default tree in forest
	    Returns : $tree
	    Args    : NONE
	    Comments: This is a	flag to	indicate that the invocant
		      is the default tree in a forest, i.e. to
		      capture the '*' token in nexus files.

       set_not_default()
	   Sets	tree to	NOT be the default tree	in a forest

	    Type    : Mutator
	    Title   : set_not_default
	    Usage   : $tree->set_not_default;
	    Function: Sets tree	to not be default tree in forest
	    Returns : $tree
	    Args    : NONE
	    Comments: This is a	flag to	indicate that the invocant
		      is the default tree in a forest, i.e. to
		      capture the '*' token in nexus files.

   TESTS
       is_default()
	   Test	if tree	is default tree.

	    Type    : Test
	    Title   : is_default
	    Usage   : if ( $tree->is_default ) {
			 # do something
		      }
	    Function: Tests whether the	invocant
		      object is	the default tree in the	forest.
	    Returns : BOOLEAN
	    Args    : NONE

       is_rooted()
	   Test	if tree	is rooted.

	    Type    : Test
	    Title   : is_rooted
	    Usage   : if ( $tree->is_rooted ) {
			 # do something
		      }
	    Function: Tests whether the	invocant
		      object is	rooted.
	    Returns : BOOLEAN
	    Args    : NONE
	    Comments: A	tree is	considered unrooted if:
		      -	set_as_unrooted	has been set, or
		      -	the basal split	is a polytomy

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::Forest::TreeRole
	   The Bio::Phylo::Forest::Tree	package	inherits from the
	   Bio::Phylo::Forest::TreeRole	package, so the	methods	defined
	   therein also	apply to trees.

       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>

perl v5.24.1			  2014-03-27	   Bio::Phylo::Forest::Tree(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

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