steac.sptree: Build a STEAC tree

In bomeara/phybase: Basic functions for phylogenetic analysis

Description

The function can build a STEAC tree from a set of gene trees.

Usage

steac.sptree(trees, speciesname, taxaname, species.structure,outgroup,method="nj") 

Arguments

trees	the gene tree vector
speciesname	species names
taxaname	taxa names
species.structure	a matrix defining the species-taxa relationship
outgroup	outgroup
method	UPGMA or NJ

Value

The function returns a STEAC tree.

Author(s)

Liang Liu [e-mail]

See Also

mrca.2nodes, mrca.nodes

Examples

#create three gene trees
treestr<-rep("",4)
treestr[1]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);"
treestr[2]<-"((((H:0.00402,G:0.00402):0.00304,C:0.00706):0.00929,O:0.01635):0.1,W:0.11635);"
treestr[3]<-"((((O:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,H:0.01635):0.1,W:0.11635);"
treestr[4]<-"((((H:0.00402,C:0.00402):0.00304,G:0.00706):0.00929,O:0.01635):0.1,W:0.11635);"

speciesname<-species.name(treestr[1])
taxaname<-speciesname
species.structure<-matrix(0,ncol=5,nrow=5)
diag(species.structure)<-1

steac.sptree(treestr, speciesname, taxaname, species.structure,outgroup="W",method="nj") 

bomeara/phybase documentation built on May 12, 2019, 11:35 p.m.