maxtree {phybase}R Documentation

Maximum Tree

Description

The function computes the Maximum Tree from multiple gene trees.

Usage

maxtree(genetreevector,spname,taxaname,species.structure)

Arguments

genetreevector a vector of gene trees
spname the species names
taxaname the names of taxa
species.structure the correspondence between species and taxa

Value

The function returns the node matrix and tree string of the maximum tree. It also returns the species names.

Author(s)

Liang Liu lliu@oeb.harvard.edu

References

Liu, L. and D.K. Pearl. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 2007, 56:504-514.

Edwards, S.V., L. Liu., and D.K. Pearl. High resolution species trees without concatenation. PNAS, 2007, 104:5936-5941.

See Also

consense, genetree.vector

Examples

genetreevector<-c("((((H:0.00302,C:0.00302):0.00304,G:0.00605):0.01029,O:0.01635):0.1,W:0.11635);","((((H:0.00402,G:0.00402):0.00304,C:0.00705):0.00929,O:0.01635):0.1,W:0.11635);");
species.structure<-matrix(0,5,5)
diag(species.structure)<-1
name<-species.name(genetreevector[1])
maxtree(genetreevector,name,name,species.structure)

[Package phybase version 1.1 Index]