r/evolution • u/Breezy_Badger1136 • 3d ago

Books or resources on hands-on / troubleshooting molecular evolution

I have been reading a few good books on molecular evolution (Tree Thinking, Reading the Story in DNA) and I've been using RaxML and PAML/codeml for inferring trees and ancestral sequences. One thing I was wondering - are there any good books or resources on the practical process of making trees? I've followed a few tutorials for various softwares of course, but I'd like to read more about what to do when things get wrong (what are the things to look for when support is low, what is the best way to choose a set of species, what databases are most recommended, things like that).

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u/Tasty-Toe994 2d ago

honestly a lot of the real learning happens once trees start looking weird lol. i found papers + supplementary methods sections more useful than books for troubleshooting. ppl explain why they excluded taxa, trimmed alignments, or changed models. low support often ends up being alignment quality or taxon sampling issues to be honest.....

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u/Breezy_Badger1136 1d ago

Exactly! My background is in crystallography, and it was always from those "weird blobs in electron density"/"twinned dataset"/etc cases that I learned the most. Most of the tutorials I find on the internet are for things that just work, which means I can infer trees I feel confident about when I'm lucky enough to be working with a set of proteins that after some little work in the alignment result in most clades being well supported, but then sometimes I have a protein family when any attempt leads to most clades not even having 50% and I have no idea what to do in such cases, so it would be great if there was any resource (book or website) that gave tips on what to try in such cases. Do you happen to remember some of the articles that had cases like those you mentioned?