exhaustiveMP | R Documentation |
This function does exhaustive and branch & bound MP searches.
exhaustiveMP(data, tree=NULL, method="branch.and.bound")
data |
is a |
tree |
an optional input tree (used only with |
method |
an optional string indicating which method to use: |
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).
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.
Liam Revell liam.revell@umb.edu
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.
mrp.supertree
, optim.parsimony
, pratchet
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