exhaustiveMP {phytools}

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 indicating which method to use: "branch.and.bound", implementing a branch-and-bound search (obviously), or "exhaustive".

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).

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.

Author(s)

Liam Revell [e-mail]

References

Felsenstein, J. (2004) Inferring Phylogenies. Sinauer.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Schliep, K. P. (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.

See Also

mrp.supertree, optim.parsimony, pratchet