Allow indels (gaps) for ancestral sequence reconstruction ASR

[bqminh]

Right now if all descending nodes of an ancestral node show gap at a site, ASR may reconstruct gap at that site for the ancestral node. But in other cases (i.e., some descending nodes have gap and some other nodes doesn't), then the ancestral state is unlikely to be gap.
Is there a way to consider gaps for the ancestral node in such cases?

Current workaround some users do is to recode gap/non-gap as 0/1 and reanalyse the data as binary data. The reconstructed 0/1 ASR can then be reconciled with the original ASR to generate indels. That means, if the 0/1 ASR shows a 0, then gap will be introduced into the original ASR. Otherwise if it is 1, then original ASR is maintained. The reconciled ASR can then be output.