the significant results means tested species is a hybrid or just have gene flow?

[CrawlingSponge]

Dear professor, Great software! I have an issue about the results about the hybrid. Here is the situation of my tests. I use there species of A, B, C and D with their species tree is (((A,B),C),D) to test that whether B is a hybrid of A and C, while the results shows that C is a hybrid of A and B with significance (P =0). My question is that is this results available? or this results just represent C maybe have gene flow with both A and B?

Another question is that, I use the population "VCF" file to transform into sequences, but the sequences is weird with non-ATCG. My question is how to use the vcf file transfer into sequences? is there any softwares?

Thank you very much and hoping for you reply!

best wish

Liu