Drop tips

[Guanyang Zhang]

How do I drop certain tips from a tree? Didn't find any info about this. A RAxML tree file is attached. I would like to drop the following tips. Thanks!

Gluconobacter_donii_Alphabacteria_AB178405.1

Pseudomonas_aeruginosa_AB037545.1

Paucibacter_toxinivorans_KX085481.1

[bena...@gmail.com]

I usually do it with the ape package first:

library(ape)
library(ggtree)

tree <- read.tree(treefile.tre)
tree <- drop.tip(tree, c("Gluconobacter_donii_Alphabacteria_AB178405.1", "Pseudomonas_aeruginosa_AB037545.1", "Paucibacter_toxinivorans_KX085481.1")) #you need to make a vector for the tips to be dropped

ggtree(tree)