parsimony {phangorn}R Documentation

Parsimony tree.

Description

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.

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.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

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)

[Package phangorn version 0.99-6 Index]