Rutger Vos > Bio-Phylo > Bio::Phylo::Forest::Tree

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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

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