Dear Klaus,
Thank you for your response. I was wondering if you could expand on how to
do this with phangorn::pml_bb(). Here's a small tree I made in Raxml with
the cytochrome b gene of a few species of birds:
library(ape)
tree <- read.tree(text =
Hi Karla,
I would recommend using raxml-ng outside of R and then reading the resulting
tree back in - the command would be something like:
raxml-ng --evaluate --msa [alignment] --tree [tree] --model GTR+G --opt-model
on --opt-branches on
The tree with the optimised branch lengths will be in
Dear all,
I have a large alignment (>3000 species) and a topology and I'd like to
estimate branch lengths on that fixed topology using a GTR+G model, but it
has been challenging computationally using optim.pml in phangorn. Any ideas
about how to speed things up?
Thanks!
Karla
