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They used maximum likelihood tree building. In Bayesian approach it’s possible to sample from a distribution of trees which can help with the uncertainty. Anywa
by f6v 3y ago
They used maximum likelihood tree building. In Bayesian approach it’s possible to sample from a distribution of trees which can help with the uncertainty. Anyway, I only have very limited knowledge on this from my evolutionary biology course.
- runeblaze 3y agoReading the paper I think they used both SVDquartets (coalescence-based explicitly for ILS) and concatenation + maximum likelihood, which is a very sane combination for the analysis. Not contradicting you here, but at their scale it is unlikely any Bayesian approach will converge, so they had to settle with whatever they had to quantify uncertainty (branch supports and others). Edit: and also the Bayesian approaches might have model mismatch, for example I am not sure what's an accurate Bayesian method that models hybridization and ILS