phangorn (version 1.2-0)

ancestral.pml: Ancestral character reconstruction.

Description

Marginal reconstruction of the ancestral character states (of the root).

Usage

ancestral.pml(object, type = "ml", ...)
ancestral.pars(tree, data, eps= 1e-08, ...)
pace(tree, data, eps= 1e-08, ...)

Arguments

object

an object of class pml

type

either "ml" or "bayes"

tree

a tree, i.e. an object of class pml

data

an object of class phyDat

eps

a small value to prevent rounding errors

...

Further arguments passed to or from other methods.

Value

• A matrix containing the

References

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

See Also

pml, parsimony, ace, root

Examples

example(NJ)
fit = pml(tree, Laurasiatherian)
anc.ml = ancestral.pml(fit, type = "ml")
anc.p = ancestral.pars(tree, Laurasiatherian)
require(seqLogo)
seqLogo(t(anc.ml[1:10,]), ic.scale=FALSE)
seqLogo(t(anc.p[1:10,]), ic.scale=FALSE)