fastMRCA: Get the MRCA (or height above the root of the MRCA) of a pair...

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa

Description

Finds the most recent common ancestor (MRCA) for a pair of tip taxa.

Usage

fastMRCA(tree, sp1, sp2)
fastHeight(tree, sp1, sp2)
fastDist(tree, sp1, sp2)

Arguments

tree	an object of class "phylo".
sp1	species one name.
sp2	species two name.

Details

Function (fastMRCA) returns the most recent common ancestor (node number) for a pair of taxa; or, in the case of fastHeight, the height above the root of the MRCA of a pair of taxa; or, in the case of fastDist, the patristic distance between a pair of taxa.

This function is mostly redundant with findMRCA (or findMRCA(...,type="height") in the case of fastHeight), but for very large trees will be considerably faster.

(Also see getMRCA in the ape package.)

Value

The node number of the MRCA, the height above the root (for fastHeight), or the patristic distance between two taxa (for fastDist).

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

getMRCA, findMRCA, mrca

Examples

tree<-pbtree(n=2000)
anc<-fastMRCA(tree,"t1","t15")

phytools documentation built on June 22, 2024, 10:39 a.m.