NAME

Bio::Tree::Statistics - Calculate certain statistics for a Tree

SYNOPSIS

use Bio::Tree::Statistics;

DESCRIPTION

This should be where Tree statistics are calculated. It was previously where statistics from a Coalescent simulation. Currently it is empty because we have not added any Tree specific statistic calculations to this module yet. We welcome any contributions.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich

Email jason AT bioperl.org

CONTRIBUTORS

Heikki Lehvaslaiho, heikki at bioperl dot org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = Bio::Tree::Statistics->new();
Function: Builds a new Bio::Tree::Statistics object 
Returns : Bio::Tree::Statistics
Args    :

assess_bootstrap

Title   : assess_bootstrap
Usage   : my $tree_with_bs = $stats->assess_bootstrap(\@bs_trees);
Function: Calculates the bootstrap for internal nodes based on
Returns : L<Bio::Tree::TreeI>
Args    : Arrayref of L<Bio::Tree::TreeI>s

cherries

Example    : cherries($tree, $node);
Description: Count number of paired leaf nodes
             in a binary tree
Returns    : integer
Exceptions : 
Args       : Bio::Tree::TreeI object
             Bio::Tree::NodeI object within the tree, optional

Commonly used statistics assume a binary tree, but this methods returns a value even for trees with polytomies.

Tree-Trait statistics

The following methods produce desciptors of trait distribution among leaf nodes within the trees. They require that a trait has to be set for each leaf node. The tag methods of Bio::Tree::Node are used to store them as key/value pairs. In this way, one tree can store more than on trait.

Trees have method add_traits() to set trait values from a file.

ps

Example    : ps($tree, $key, $node);
Description: Calculates Parsimony Score (PS) from Fitch 1971
             parsimony algorithm for the subtree a defined
             by the (internal) node.
             Node defaults to the root.
Returns    : integer, 1< PS < n, where n is number of branches
Exceptions : leaf nodes have to have the trait defined
Args       : Bio::Tree::TreeI object
             trait name string
             Bio::Tree::NodeI object within the tree, optional

Fitch, W.M., 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20, 406–416.

ai

Example    : ai($tree, $key, $node);
Description: Calculates the Association Index (AI) of Whang et
             al. 2001 for the subtree defined by the (internal)
             node.  Node defaults to the root.
Returns    : real
Exceptions : leaf nodes have to have the trait defined
Args       : Bio::Tree::TreeI object
             trait name string
             Bio::Tree::NodeI object within the tree, optional

Association index (AI) gives a more fine grained results than PS since the result is a real number. ~0 <= AI.

Wang, T.H., Donaldson, Y.K., Brettle, R.P., Bell, J.E., Simmonds, P., 2001. Identification of shared populations of human immunodeficiency Virus Type 1 infecting microglia and tissue macrophages outside the central nervous system. J. Virol. 75 (23), 11686–11699.

mc

Example    : mc($tree, $key, $node);
Description: Calculates the Monophyletic Clade (MC) size statistics
             for the subtree a defined by the (internal) node.
             Node defaults to the root;
Returns    : hashref with trait values as keys
Exceptions : leaf nodes have to have the trait defined
Args       : Bio::Tree::TreeI object
             trait name string
             Bio::Tree::NodeI object within the tree, optional

* Monophyletic Clade (MC) size statistics by Salemi at al 2005. It is calculated for each trait value. 1<= MC <= nx, where nx is the number of tips with value x:

pick the internal node with maximim value for
   number of of tips with only trait x

MC was defined by Parker et al 2008.

Salemi, M., Lamers, S.L., Yu, S., de Oliveira, T., Fitch, W.M., McGrath, M.S., 2005. Phylodynamic analysis of Human Immunodeficiency Virus Type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J. Virol. 79 (17), 11343–11352.

Parker, J., Rambaut A., Pybus O., 2008. Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty Infection, Genetics and Evolution 8 (2008), 239–246.

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq