How to get the outgroup of a rooted tree in R

Question

[Gon]

Dear all,

I need to identify the outgroup sequence(s) in a series of phylogenetic rooted trees. I've been trying to look for any function in ape or phangorn that does this, but so far I haven't found one. Any ideas?

Thanks!

Gon

Answer 1

[Brice Sarver]

A lot of trees are read in and assumed to be unrooted or rooted on the first taxon, or they can be rooted on the taxon closest to the MRCA of the tree (sometimes with a multifurcation). It really depends on the program/package you're using.

You might have success looking at the last taxon in your tip.label attribute:

library(ape)

a <- read.tree("your_tree.tre")
a$tip.label[length(a$tip.label)]

This might be in a trifurcation with the first taxon, too:

a$tip.label[1]

Alternatively, without getting into too much detail about figuring which is the root edge, etc., try this for a quick answer using R:

a <- read.tree("your_tree.tre")
plot(a)

#now, select the root by clicking on the tree
identify.phylo(a)

#this will return the position of the taxon you clicked on in the vector a$tip.label

[Gon]

Thanks! Ideally I would've liked to find a function or a more automatized method, but sometimes that's asking too much.

I will use your recommendation, thanks a lot.