bin.multiPhylo: Bin Trees
In distory: Distance Between Phylogenetic Histories

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/bin.multiPhylo.R

Bins trees according to branching topology.

1	bin.multiPhylo(treelist)

treelist

A list of trees that can be passed to dist.phylo (see the help for dist.phylo for acceptable formats).

Bins trees according to branching topology. Two trees are considered to have the same topology if the same set of partitions of tips are produced by the edges, which corresponds to the same branching up to rearrangement of tips.

Returns a numeric vector of bin ids. Bin ids are assigned in order of the first tree in that bin, that is, the first k unique trees in the list passed will be assigned bins 1..k in order of appearance.

John Chakerian

Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.

dist.multiPhylo

data(woodmouse)
otree <- root(fastme.ols(dist.dna(woodmouse)), "No305", resolve.root=TRUE)
breps <- 500

trees <- boot.phylo(otree, woodmouse, B=breps, function(x)
        root(fastme.ols(dist.dna(x)), "No305", resolve.root=TRUE),trees=TRUE)

combined.trees <- c(list(otree), trees$trees)

bin.multiPhylo(combined.trees)