Hey @joqb, I'm hoping to provide something similar eventually, the problem with the pyrad alleles file is that the alleles are only phased correctly when we enforce that reads must align almost completely, i.e., they are not staggered in their overlap. So the alleles are correct for RAD data, because the reads match up perfectly on their left side, however, staggered overlaps are common in other data sets that use very common cutters, like ezRAD and some GBS, and especially so when R1 and R2 reads merge. So we needed to change to an alternative way of coding the alleles so that we can store both phased and unphased alleles, and its just taking a while to do. So for now we are only providing unphased alleles, although we do save the estimated number of alleles for each locus. This information is kind of hidden under the hood at the moment though.