- AUTHOR - Jason Stajich
Bio::Tree::Statistics - Calculate certain statistics for a Tree
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.
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Email jason AT bioperl.org
Heikki Lehvaslaiho, heikki at bioperl dot org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::Tree::Statistics->new(); Function: Builds a new Bio::Tree::Statistics object Returns : Bio::Tree::Statistics Args :
Title : assess_bootstrap Usage : my $tree_with_bs = $stats->assess_bootstrap(\@bs_trees); Function: Calculates the bootstrap for internal nodes based on Returns : L<Bio::Tree::TreeI> Args : Arrayref of L<Bio::Tree::TreeI>s
Example : cherries($tree, $node); Description: Count number of paired leaf nodes in a binary tree Returns : integer Exceptions : Args : Bio::Tree::TreeI object Bio::Tree::NodeI object within the tree, optional
Commonly used statistics assume a binary tree, but this methods returns a value even for trees with polytomies.
The following methods produce desciptors of trait distribution among leaf nodes within the trees. They require that a trait has to be set for each leaf node. The tag methods of Bio::Tree::Node are used to store them as key/value pairs. In this way, one tree can store more than on trait.
Trees have method add_traits() to set trait values from a file.
Example : ps($tree, $key, $node); Description: Calculates Parsimony Score (PS) from Fitch 1971 parsimony algorithm for the subtree a defined by the (internal) node. Node defaults to the root. Returns : integer, 1< PS < n, where n is number of branches Exceptions : leaf nodes have to have the trait defined Args : Bio::Tree::TreeI object trait name string Bio::Tree::NodeI object within the tree, optional
Fitch, W.M., 1971. Toward deﬁning the course of evolution: minimal change for a speciﬁc tree topology. Syst. Zool. 20, 406–416.
Example : ai($tree, $key, $node); Description: Calculates the Association Index (AI) of Whang et al. 2001 for the subtree defined by the (internal) node. Node defaults to the root. Returns : real Exceptions : leaf nodes have to have the trait defined Args : Bio::Tree::TreeI object trait name string Bio::Tree::NodeI object within the tree, optional
Association index (AI) gives a more fine grained results than PS since the result is a real number. ~0 <= AI.
Wang, T.H., Donaldson, Y.K., Brettle, R.P., Bell, J.E., Simmonds, P., 2001. Identiﬁcation of shared populations of human immunodeﬁciency Virus Type 1 infecting microglia and tissue macrophages outside the central nervous system. J. Virol. 75 (23), 11686–11699.
Example : mc($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.
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