Question about the

[Orz-CQ]

Hi Paul, Amazing software!

I have several questions about the HyDe. I see the input data should be diploid data or ambiguous sites. But here I have a diploid species and tetraploid species, and through hybridization we got a triploid species.

I have assembled the phased genome of the three species. After whole genome alignment, I attend to test if the triploid species indeed generated by the cross-breeding by the diploid species and tetraploid species.

Could I use the all phased genome alignments as input? For the map file, diploid may contain hap1 and hap2; the triploid may contain hap1, hap2 and hap3, et al. It is correct to perform the analysis?