steac.sptree {phybase} | R Documentation |
The function can build a STEAC tree from a set of gene trees.
steac.sptree(trees, speciesname, taxaname, species.structure,outgroup,method="nj")
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 |
The function returns a STEAC tree.
Liang Liu lliu@oeb.harvard.edu
#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")