phytools (version 0.2-40)

exhaustiveMP: Exhaustive and branch & bound MP optimization

Description

This function does exhaustive and branch & bound MP searches.

Usage

exhaustiveMP(data, tree=NULL, method="branch.and.bound")

Arguments

data

is a phyDat (Schliep 2011) object containing DNA or other data.

tree

an optional input tree (used only with method="branch.and.bound").

method

an optional string indicatingn method to use: "branch.and.bound" or "exhaustive".

Value

• a "phylo" or "multiPhylo" object that is the MP tree or set of MP trees. It also returns the parsimony scores in attr(trees,"pscore") or attr(trees[[i]],"pscore") for the ith tree.

Details

Should probably not be used for more than about 8 species (and definitely not more than 10 species). Performs parsimony calculations using parsimony in the "phangorn" package (Schliep 2011).

References

Felsenstein, J. 2004. Inferring Phylogenies. Sinauer. Schliep, K. P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.

See Also

mrp.supertree, optim.parsimony, pratchet