phangorn (version 1.0-2)

parsimony: Parsimony tree.

Description

parsimony returns the parsimony score of a tree. optim.parsimony tries to find the maximum parsimony tree using Nearest Neighbor Interchange (NNI) rearrangements. pace returns a (logical) matrix of the ancestral states of the root node.

Usage

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, ...)

Arguments

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.

Value

• parsimony returns the maximum parsimony score (pscore). optim.parsimony returns a tree after NNI rearrangements.

References

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

See Also

nni, NJ, pml

Examples

data(Laurasiatherian)
dm = dist.logDet(Laurasiatherian)
tree = NJ(dm)
parsimony(tree, Laurasiatherian)
ptree <- optim.parsimony(tree, Laurasiatherian)