midpoint.root: Midpoint root a phylogeny

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

Midpoint root a phylogeny

Description

These functions midpoint root a rooted or unrooted tree (Farris 1972).

Usage

midpoint_root(tree)
## S3 method for class 'root'
midpoint(tree, node.labels="support", ...)

Arguments

tree	an object of class "phylo".
node.labels	argument to be passed to midpoint.
...	optional arguments to be passed to midpoint.

Details

Midpoint rooting involves locating the midpoint of the longest path between any two tips and putting the root in that location.

The function midpoint_root performs the same operation as midpoint in the phangorn package, but uses no phangorn (Schliep, 2011) code internally.

The function midpoint.root is a pseudo S3 method for the object class "root" that exists because when midpoint was created in phangorn it was not defined as a generic method. This function merely points to midpoint and is being deprecated out.

Value

An object of class "phylo" containing a rooted phylogenetic tree.

Author(s)

Liam Revell [e-mail]

References

Farris, J. (1972) Estimating phylogenetic trees from distance matrices. American Naturalist, 106, 645-667.

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.

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

Schliep K. P. (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.

See Also

midpoint, reroot, root

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