sctree {phybase} | R Documentation |
The function computes the shallowest coalescence tree from multiple gene trees.
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@oeb.harvard.edu
Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
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)