maxtree: Maximum Tree
In bomeara/phybase: Basic functions for phylogenetic analysis

Description Usage Arguments Value Author(s) References See Also Examples

The function computes the Maximum Tree from multiple gene trees.

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

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

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

Liang Liu lliu@uga.edu

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.

consense, genetree.vector

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)