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Bio-Phylo-0.04
River stage two • 9 direct dependents • 18 total dependents
8 ++
/ Bio::Phylo::Trees::Tree

NAME

Bio::Phylo::Trees::Tree - An object-oriented module for phylogenetic trees

SYNOPSIS

 use Bio::Phylo::Trees::Tree;
 my $tree = new Bio::Phylo::Trees::Tree;

DESCRIPTION

The object models a phylogenetic tree, which consists of Bio::Phylo::Trees::Node objects.

METHODS

CONSTRUCTOR

new()
 Type    : Constructor
 Title   : new
 Usage   : my $tree = new Bio::Phylo::Trees::Tree;
 Function: Instantiates a Bio::Phylo::Trees::Tree object.
 Returns : A Bio::Phylo::Trees::Tree object.
 Args    : none.

TREE POPULATION

_analyze()
 Type    : Internal method
 Title   : _analyze
 Usage   : $tree->_analyze;
 Function: Traverses the tree, creates references to first_daughter,
           last_daughter, next_sister and previous_sister.
 Returns : A Bio::Phylo::Trees::Tree object.
 Args    : none.
 Comments: This method only looks at the parent, so theoretically
           one could mess around with the
           Bio::Phylo::Trees::Node::parent(Bio::Phylo::Trees::Node) method and
           subsequently call Bio::Phylo::Trees::Tree::_analyze to overwrite old
           (and wrong) child and sister references with new (and correct) ones.

QUERIES

get_terminals()
 Type    : Query
 Title   : get_terminals
 Usage   : $tree->get_terminals;
 Function: Retrieves all terminal nodes in
           the current Bio::Phylo::Trees::Tree object.
 Returns : A list of Bio::Phylo::Trees::Node objects.
 Args    : none.
 Comments: If the tree is valid, this method retrieves the same set
           of nodes as $node->get_terminals($root). However, because
           there is no recursion it may be faster. Also, the node
           method by the same name does not see orphans.
get_internals()
 Type    : Query
 Title   : get_internals
 Usage   : $tree->get_internals;
 Function: Retrieves all internal nodes in the current Bio::Phylo::Trees::Tree
           object.
 Returns : A list of Bio::Phylo::Trees::Node objects.
 Args    : none.
 Comments: If the tree is valid, this method retrieves the same set
           of nodes as $node->get_internals($root). However, because
           there is no recursion it may be faster. Also, the node
           method by the same name does not see orphans.
get_root()
 Type    : Query
 Title   : get_root
 Usage   : $tree->get_root;
 Function: Retrieves the first orphan in the current Bio::Phylo::Trees::Tree
           object - which should be the root.
 Returns : A Bio::Phylo::Trees::Node object.
 Args    : none.

TESTS

is_binary()
 Type    : Test
 Title   : is_binary
 Usage   : $tree->is_binary;
 Function: Tests whether the current Bio::Phylo::Trees::Tree
           object is bifurcating.
 Returns : BOOLEAN.
 Args    : none.
is_ultrametric($margin)
 Type    : Test
 Title   : is_ultrametric
 Usage   : $tree->is_ultrametric(0.01);
 Function: Tests whether the current Bio::Phylo::Trees::Tree object is
           ultrametric.
 Returns : BOOLEAN.
 Args    : Optional margin between pairwise comparisons (default = 0).
 Comments: The test is done by performing all pairwise comparisons for
           root-to-tip path lengths. Since many programs introduce
           rounding errors in branch lengths the optional argument is
           available to test TRUE for nearly ultrametric trees. For
           example, a value of 0.01 indicates that no pairwise
           comparison may differ by more than 1%. Note: behaviour is
           undefined for negative branch lengths.
is_monophyletic(\@ARRAY, Bio::Phylo::Trees::Node)
 Type    : Test
 Title   : is_monophyletic
 Usage   : $tree->is_monophyletic(\@tips, $outgroup);
 Function: Tests whether the set of \@tips is
           monophyletic w.r.t. $outgroup.
 Returns : BOOLEAN.
 Args    : A reference to a list of nodes, and a node.
 Comments: This method is essentially the
           same as Bio::Phylo::Trees::Node::is_outgroup_of.

CALCULATIONS

calc_tree_length()
 Type    : Calculation
 Title   : calc_tree_length
 Usage   : $tree->calc_tree_length;
 Function: Calculates the sum of all branch
           lengths (i.e. the tree length).
 Returns : FLOAT
 Args    : none.
calc_tree_height()
 Type    : Calculation
 Title   : calc_tree_height
 Usage   : $tree->calc_tree_height;
 Function: Calculates the height of the tree.
 Returns : FLOAT
 Args    : none.
 Comments: For ultrametric trees this method returns the height, but this is
           done by averaging over all root-to-tip path lengths, so for
           additive trees the result should consequently be interpreted
           differently.
calc_number_of_nodes()
 Type    : Calculation
 Title   : calc_number_of_nodes
 Usage   : $tree->calc_number_of_nodes;
 Function: Calculates the number of nodes (internals AND terminals).
 Returns : INT.
 Args    : none.
calc_number_of_terminals()
 Type    : Calculation
 Title   : calc_number_of_terminals
 Usage   : $tree->calc_number_of_terminals;
 Function: Calculates the number of terminal nodes.
 Returns : INT.
 Args    : none.
calc_number_of_internals()
 Type    : Calculation
 Title   : calc_number_of_internals
 Usage   : $tree->calc_number_of_internals;
 Function: Calculates the number of internal nodes.
 Returns : INT.
 Args    : none.
calc_total_paths()
 Type    : Calculation
 Title   : calc_total_paths
 Usage   : $tree->calc_total_paths;
 Function: Calculates the sum of all root-to-tip path lengths.
 Returns : FLOAT.
 Args    : none.
calc_redundancy()
 Type    : Calculation
 Title   : calc_redundancy
 Usage   : $tree->calc_redundancy;
 Function: Calculates the amount of shared
           (redundant) history on the total.
 Returns : FLOAT.
 Args    : none
 Comments: Redundancy is calculated as
 1 / ( treelength - height / ( ntax * height - height ) )
calc_imbalance()
 Type    : Calculation
 Title   : calc_imbalance
 Usage   : $tree->calc_imbalance;
 Function: Calculates Colless' coefficient of tree imbalance.
 Returns : FLOAT.
 Args    : none
 Comments: As described in Colless, D.H., 1982. The theory and practice of
           phylogenetic systematics. Systematic Zoology 31(1): 100-104
calc_fiala_stemminess()
 Type    : Calculation
 Title   : calc_stemminess
 Usage   : $tree->calc_stemminess;
 Function: Calculates stemminess measure Fiala and Sokal (1985).
 Returns : FLOAT.
 Args    : none
 Comments: As described in Fiala, K.L. and R.R. Sokal, 1985. Factors determining
           the accuracy of cladogram estimation: evaluation using computer
           simulation. Evolution, 39: 609-622
calc_rohlf_stemminess()
 Type    : Calculation
 Title   : calc_stemminess
 Usage   : $tree->calc_rohlf_stemminess;
 Function: Calculates stemminess measure from Rohlf et al. (1990).
 Returns : FLOAT.
 Args    : none
 Comments: As described in Rohlf, F.J., W.S. Chang, R.R. Sokal, J. Kim, 1990.
           Accuracy of estimated phylogenies: effects of tree topology and
           evolutionary model. Evolution, 44(6): 1671-1684
calc_resolution()
 Type    : Calculation
 Title   : calc_resolution
 Usage   : $tree->calc_resolution;
 Function: Calculates the total number of internal nodes over the
           total number of internal nodes on a fully bifurcating
           tree of the same size.
 Returns : FLOAT.
 Args    : none
calc_branching_times()
 Type    : Calculation
 Title   : calc_branching_times
 Usage   : $tree->calc_branching_times;
 Function: Returns a two-dimensional array. The first dimension
           consists of the "records", so that in the second
           dimension $AoA[$first][0] contains the internal node
           references, and $AoA[$first][1] the branching time
           of the internal node. The records are orderered from
           root to tips by time from the origin.
 Returns : SCALAR[][] or FALSE.
 Args    : none
calc_ltt()
 Type    : Calculation
 Title   : calc_ltt
 Usage   : $tree->calc_ltt;
 Function: Returns a two-dimensional array. The first dimension
           consists of the "records", so that in the second dimension
           $AoA[$first][0] contains the internal node references, and
           $AoA[$first][1] the branching time of the internal node,
           and $AoA[$first][2] the cumulative number of lineages over
           time. The records are orderered from root to tips by
           time from the origin.
 Returns : SCALAR[][] or FALSE.
 Args    : none

TREE MANIPULATION

ultrametricize()
 Type    : Tree manipulator
 Title   : ultrametricize
 Usage   : $tree->ultrametricize();
 Function: Sets all root-to-tip path lengths equal by stretching
           all terminal branches to the height of the tallest node.
 Returns : A Bio::Phylo::Trees::Tree object.
 Args    : none.
 Comments: This method is analogous to the 'ultrametricize' command
           in Mesquite, i.e. no rate smoothing or anything like that
           happens, just a lengthening of terminal branches.
scale($height)
 Type    : Tree manipulator
 Title   : scale
 Usage   : $tree->scale($height);
 Function: Scales the tree to the specified height.
 Returns : A Bio::Phylo::Trees::Tree object.
 Args    : $height = a numerical value indicating root-to-tip path length.
 Comments: This method uses the $tree->calc_tree_height method, and so for
           additive trees the *average* root-to-tip path length is scaled to
           $height (i.e. some nodes might be taller than $height, others
           shorter).
resolve()
 Type    : Tree manipulator
 Title   : resolve
 Usage   : $tree->resolve();
 Function: Breaks polytomies by inserting additional internal nodes orderered
           from left to right.
 Returns : A binary Bio::Phylo::Trees::Tree object.
 Args    :
 Comments:
prune_tips()
 Type    : Tree manipulator
 Title   : prune_tips
 Usage   : $tree->prune_tips(@taxa);
 Function: Prunes specified taxa from invocant.
 Returns : A pruned Bio::Phylo::Trees::Tree object.
 Args    : A list of taxa.
 Comments:
keep_tips()
 Type    : Tree manipulator
 Title   : keep_tips
 Usage   : $tree->keep_tips(@taxa);
 Function: Keeps specified taxa from invocant.
 Returns : A pruned Bio::Phylo::Trees::Tree object.
 Args    : A list of taxa.
 Comments:
negative_to_zero()
 Type    : Tree manipulator
 Title   : negative_to_zero
 Usage   : $tree->negative_to_zero;
 Function: Converts negative branch lengths to zero.
 Returns : A Bio::Phylo::Trees::Tree object without negative branch lengths.
 Args    : None.
 Comments:
remove_unbranched_internals()
 Type    : Tree manipulator
 Title   : remove_unbranched_internals
 Usage   : $tree->remove_unbranched_internals();
 Function: Collapses internal nodes with fewer than 2 children.
 Returns : A Bio::Phylo::Trees::Tree object.
 Args    : None.
 Comments:

CONTAINER

container
 Type    : Internal method
 Title   : container
 Usage   : $tree->container;
 Function:
 Returns : SCALAR
 Args    :
container_type
 Type    : Internal method
 Title   : container_type
 Usage   : $tree->container_type;
 Function:
 Returns : SCALAR
 Args    :

AUTHOR

Rutger Vos, <rvosa@sfu.ca> http://www.sfu.ca/~rvosa/

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.