parsimony {phangorn} | R Documentation |
parsimony
returns the parsimony score of a tree.
optim.parsimony
tries to find the mamimum parsimony tree using NNI
rearrangements. pace
returns a (logical) matrix of the ancestral states
of the root node.
parsimony(tree, data, method="sankoff", ...) optim.parsimony(tree, data, cost=NULL, ...) fitch(tree, data, site = FALSE) sankoff(tree, data, cost = NULL, site = FALSE) pace(tree, data, ...)
data |
A object of class phyDat containing (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. |
site |
logical, if TRUE site wise parsimony scores are returned. |
... |
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 klaus.schliep@gmail.com
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)