I fixed the ancestral genome bug (https://github.com/DessimozLab/pyham/issues/7) by overwriting extant genomes that are ancestral with an ancestral genome. I don't know if this is the optimal solution, but seems to be an improvement, since you can at least run though the analysis without getting a fatal error. I believe I found another bug in def set_MRCA where it appears to go up two levels instead of one to find the most recent common ancestor.
I fixed the ancestral genome bug (https://github.com/DessimozLab/pyham/issues/7) by overwriting extant genomes that are ancestral with an ancestral genome. I don't know if this is the optimal solution, but seems to be an improvement, since you can at least run though the analysis without getting a fatal error. I believe I found another bug in def set_MRCA where it appears to go up two levels instead of one to find the most recent common ancestor.