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Bio::Tree::Statistics.3pm
Langue: en
Version: 2009-02-27 (fedora - 05/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tree::Statistics - Calculate certain statistics for a TreeSYNOPSIS
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.orgCONTRIBUTORS
Heikki Lehvaslaiho, heikki at bioperl dot orgAPPENDIX
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, $node); Description: Calculates Parsimony Score (PS) from Fitch 1971 parsimony algorithm for the subtree a defined by the (internal) node. Node defaults to the root. Returns : integer, 1< PS < n, where n is number of branches Exceptions : leaf nodes have to have the trait defined Args : Bio::Tree::TreeI object trait name string Bio::Tree::NodeI object within the tree, optional
Fitch, W.M., 1971. Toward dei.XXning the course of evolution: minimal change for a specii.XXc tree topology. Syst. Zool. 20, 406aXX416.
ai
Example : ai($tree, $key, $node); Description: Calculates the Association Index (AI) of Whang et al. 2001 for the subtree defined by the (internal) node. Node defaults to the root. Returns : real Exceptions : leaf nodes have to have the trait defined Args : Bio::Tree::TreeI object trait name string Bio::Tree::NodeI object within the tree, optional
Association index (AI) gives a more fine grained results than PS since the result is a real number. ~0 <= AI.
Wang, T.H., Donaldson, Y.K., Brettle, R.P., Bell, J.E., Simmonds, P.,
2001. Identii.XXcation of shared populations of human immunodei.XXciency
Virus Type 1 infecting microglia and tissue macrophages outside the
central nervous system. J. Virol. 75 (23), 11686aXX11699.
mc
Example : mc($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 Immunodei.XXciency Virus Type 1 in
distinct brain compartments provides a model for the neuropathogenesis of
AIDS. J. Virol. 79 (17), 11343aXX11352.
Parker, J., Rambaut A., Pybus O., 2008. Correlating viral phenotypes
with phylogeny: Accounting for phylogenetic uncertainty Infection,
Genetics and Evolution 8 (2008), 239aXX246.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre