Milan Malinsky

Hi Trev I would have to see a little of your VCF and the SETS.txt file to be sure how this is processed. I think that all should be fine...

This is not possible at the moment. I thought about implementing it, but the problem is then that different equally-sized physical widows then have different amounts of information (informative SNPs)...

Hi Tomas Thanks for this info. I checked, and should indeed be explicitly included to compile with GCC 11. So I just added the line I think your other error...

Yes, exactly, the newer versions (since July 2022) should be able to handle arbitrary ploidy, including mixed ploidy, based on request from Nélida Padilla and Filip Kolar. Did I not...

Hi everyone ... Both f_d and f_dM were developed to look for candidate introgressed regions in cases where the genome-wide D statistic is significantly positive (suggesting gene-flow between P3 and...

One more thought, with regards to the cutoffs for the positive f_d and f_dM. It is not clear what the best cutoff would be. Top 5% like @RezaFahi is an...

This is perfect, a big thank you @jeromekelleher and @gtsambos

Hi, yes, you’re right, a previous “simplification” of the code broke Dquartets. I think I fixed it now in r55. Please check and let me know if all the output...

Dear Scott I can think of a number of possible reasons: 1) Introgression went both from P3 -> P1 and P3 -> P2 in about equal proportions. Then D is...

One more thought: I see that "clustering_KS_p-val2" is not significant in the example above. This is interesting, because "clustering_KS_p-val2" should be robust to mutation rate variation. At the same time,...