SNAPP with phased or unphased data

[Ming-Hsun Chou]

Hello!

I'm trying to use SNAPP for species tree inference for diploid organisms. However, I'm not sure if SNAPP can handle phased SNPs. Although some studies (e.g., https://doi.org/10.1016/j.ympev.2022.107396) applied phased SNPs for SNAPP, it's unclear how to set up parameters for phased data.

So, my question is that is SNAPP able to analyze phased SNPs, because I seemed unable to set up ploidy in BEAUti for SNAPP?

Thank you!