Can I randomly select one sequence per species out of a homologous group to make a species tree?
I have list of 105 species and their genomes. I want to make a species tree out of this data and want to run IQTree2) but am a little confused about one of the steps. What do I do if I end up with zero homologous groups with single copies only? I ran clustering on the data with OrthoFinder and have some 20k homologous groups but none with single copies only.
Can I take a homologous group with all species present and select one para-log per species randomly? or this completely wrong?
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