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 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/