Ploidy in Starbeast and EBSP

[Dylan O'Hearn]

Hello,

When using phased haplotypes (i.e., the two haplotypes of a nuclear locus in a diploid individual are represented by two separate sequences), what ploidy setting should be used in Starbeast and for extended Bayesian skyline plots?  I know "2" is usually recommended for nuclear loci, but it seems like that should actually depend on whether you're talking about two phased haplotypes per individual or one unphased consensus sequence per individual.