Paul Blischak

Hi He! And thanks for using HyDe! As you've noted, HyDe can't determine the directionality of hybridization, but I think that there are other methods that can. I would suggest...

Hi Liu, Based on your results, it looks like there may be some evidence for hybridization among the ancestral lineages of the taxa you are testing. I think that is...

Hi Pedro -- this is definitely an interesting situation. Would you mind sharing a little bit more about your data set so that I can hopefully help out a bit...

Thanks! This sounds like a really cool system! I think what you are describing using the phased chromosomes/haplotypes as "individuals" from the same population or species makes sense. So you...

I'm wondering if something with the ordering of the taxa in the map file and data file is causing an issue. Are the samples in the same order in both?...

The map file I put above was just a rough example so if the data don't match it exactly it could definitely cause some issues. That map file also doesn't...

Okay, so a couple of things are sticking out to me. First, are you putting the string "sequence length" in your phylip file? If so, it needs to be a...

It looks like all of your site patterns are AAAA, so the program is saying that there is no variation in your data. If you want to send me your...

From your results there are no SSBW, FJC, or ZJC populations so I'm not sure I can help determine if something is a hybrid here. Your results definitely make it...

Hi Liu -- thanks for using HyDe! Depending on how big the estimate of gamma is can be a better indicator of if something is a hybrid or if there...