coal.sptree: Estimating species trees using average coalescence times

In bomeara/phybase: Basic functions for phylogenetic analysis

Description

For a given set of gene trees, the UPGMA tree is constructed from the distance matrix based on the average coalescence times among taxa.

Usage

coal.sptree(trees, speciesname, nspecies, outgroup=1)

Arguments

trees	a vector of trees in newick format
speciesname	species names
nspecies	number of species
outgroup	the node number of the species used to root the tree

Details

If the gene trees are not clocklike trees, they are first converted to clock trees using function noclock2clock and then construct a distance matrix in which the entries are twice the coalescence times among species. The distance matrix is used to build an UPGMA tree as the estimate of the species tree. This function is different from steac.sptree in that steac.sptree uses nucleotide distances to construct distance matrix.

Value

The function returns the tree node matrix and the estimate of the species tree.

Author(s)

Liang Liu

See Also

See also to steac.sptree

Examples

data(rooted.tree)
genetrees<-rooted.tree
spname<-species.name(genetrees[1])
coal.sptree(genetrees,spname,nspecies=4,outgroup=4)

bomeara/phybase documentation built on May 12, 2019, 11:35 p.m.