star.sptree: Build a STAR tree

In bomeara/phybase: Basic functions for phylogenetic analysis

Description

The function can build a STAR tree from a set of gene trees. Although STAR can handle missing sequences, it requires that all possible pairs of species (n choose 2) should appear in at least one gene tree. Otherwise, STAR cannot calculate the pairwise distances among species.

Usage

star.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	UPGMA1, UPGMA2, or NJ

Value

The function returns a STAR 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

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

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