sptree.maxtree: Maximum Tree

In lliu1871/phybase: Basic functions for phylogenetic analysis

Maximum Tree

Description

The function computes the Maximum Tree from multiple gene trees.

Usage

sptree.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 [e-mail]

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.

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])
sptree.maxtree(genetreevector,name,name,species.structure)

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.