sctree {phybase}R Documentation

Shallowest Coalescence Tree

Description

The function computes the shallowest coalescence tree from multiple gene trees.

Usage

sctree(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

Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.

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])
sctree(genetreevector,name,name,species.structure)

[Package phybase version 1.1 Index]