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
[alignment].raxml.bestTree.
Cheers,
Nat
________________________________
From: R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of Karla Shikev
<karlashi...@gmail.com>
Sent: Tuesday, March 5, 2024 7:17:00 PM
To: R Sig Phylo Listserv <r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] estimating BLs on a fixed topology
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
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