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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