Yes we tried pSONIC and found it improved things calls over short phylogenetic distances (e.g. within brassicas), but not much over larger ones (probably because of extensive rearrangement?)
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Milton Tan
Haven't seen Alphafold used in orthology prediction but for sure there are a handful of methods incorporating synteny/collinearity. I don't think there's a top dog here yet, but pSONIC is one I've heard of. Unfortunately haven't gotten a chance to try it yet. academic.oup.com/g3journal/ar...
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