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Man Pages


Manual Reference Pages  -  BIO::PHYLO::FOREST::TREE (3)

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NAME

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

CONTENTS

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:

<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB> and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics <B>12B>:63. <http://dx.doi.org/10.1186/1471-2105-12-63>

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perl v5.20.3 BIO::PHYLO::FOREST::TREE (3) 2014-03-27

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