rerootPhylo: Reroot Phylo

In revbayes/RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

Reroot Phylo

Description

Reroots a phylogeny given an outgroup taxon or clade

Usage

rerootPhylo(tree, outgroup)

Arguments

tree	(list of lists of treedata objects; no default) Name of a list of lists of treedata objects, such as produced by readTrees().
outgroup	(character, no default) Name of the outgroup(s). Either a single taxon name or a character vector of length two to specify a clade; in this case the root will be placed at the midpoint of the branch subtending the two taxa's MRCA. Modified from phytools::reroot().

Details

Modifies a tree object by rerooting using a specified outgroup taxon or clade. Places the root at the midpoint of the branch subtending the outgroup. If the input contains multiple trees, all trees will be rerooted.

Value

returns a list of list of treedata objects, with the trees rooted.

See Also

phytools: reroot.

Examples

file <- system.file("extdata",
                    "sub_models/primates_cytb_GTR_MAP.tre",
                    package="RevGadgets")
tree <- readTrees(paths = file)
# root with one taxon
tree_rooted <- rerootPhylo(tree = tree, outgroup = "Galeopterus_variegatus")
# root with clade, specified by two taxa
tree_rooted <- rerootPhylo(tree = tree,
                           outgroup = c("Varecia_variegata_variegata",
                                        "Propithecus_coquereli"))

revbayes/RevGadgets documentation built on Jan. 19, 2024, 3:29 p.m.