sctree: Shallowest Coalescence Tree
In bomeara/phybase: Basic functions for phylogenetic analysis

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

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

1	sctree(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

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

consense, genetree.vector

genetreevector<-c("((((H:0.2,C:0.2):0.3,G:0.5):0.9,O:1.4):0.1,W:1.5);",
"((((H:0.2,G:0.2):0.4,C:0.6):0.9,O:1.5):0.1,W:1.6);");
species.structure<-matrix(0,5,5)
diag(species.structure)<-1
name<-species.name(genetreevector[1])
sctree(genetreevector,name,name,species.structure)