Exhaustive and branch & bound.
exhaustiveMP(): this does exhaustive and branch & bound MP tree searches.
Input
trees<-exhaustiveMP(data,tree=NULL,method="branch.and.bound")
"data" is a phyDat (Schliep 2011) object containing DNA or other data;
"tree" is an input tree (used only with method="branch.and.bound");
"method" can be "exhaustive" or "branch.and.bound" (defaults to the latter).
Function requires the "ape" (Paradis & Strimmer 2004) and "phangorn" (Schliep 2011) packages.
Output
exhaustiveMP() returns a "phylo" or "multiPhylo" object that is the MP tree or set of MP trees (the latter is only guaranteed if method="exhaustive").
It also returns the parsimony scores. To see these, type: attr(trees,"pscore") or attr(trees[[i]],"pscore") for the ith tree in a "multiPhylo" object.
Citation
Function written by Liam J. Revell 2011.
References:
Felsenstein, J. 2004. Inferring Phylogenies. Sinauer.
Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.
Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics 27: 592-593.
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Last modified Apr. 3, 2011.