parsimony {phangorn} | R Documentation |
parsimony
returns the parsimony score of a tree.
optim.parsimony
tries to find the mamximum parsimony tree using NNI
rearrangements.
parsimony(tree, data, method="sankoff", ...) optim.parsimony(tree, data, cost=NULL, ...)
data |
A (dna) sequences. |
tree |
tree to start the nni search from. |
method |
one of 'fitch' or 'sankoff'. |
cost |
A cost matrix for the transitions between two states. |
... |
Further arguments passed to or from other methods. |
parsimony
returns the maximum parsimony score (pscore).
optim.parsimony
returns a tree after NNI rearrangements.
Klaus Schliep K.P.Schliep@massey.ac.nz
Felsenstein, J. (2004). Inferring Phylogenies. Sinauer Associates, Sunderland.
data(Laurasiatherian) dm = dist.logDet(Laurasiatherian) tree = NJ(dm) parsimony(tree, Laurasiatherian) ptree <- optim.parsimony(tree, Laurasiatherian)