hyde conflict with tree results #51
Description
Dear Author,
Thank you for providing such a convenient and powerful tool.
I am analyzing a hybridization study involving three species: A, B, and C, and an outgroup. When constructing the tree, I found that B might be a hybrid species (with a 1:1 ratio of A-B and C-B), and the results from QuIBL also suggest hybridization/introgression. However, when I used Hyde, the analysis shows that C is the hybrid species, and each of its parent species contributes 50% (i.e., gamma: 0.5).
I have checked the input data, parameters, and the running method, and I couldn't identify any issues. Could you please help me understand what might be causing this discrepancy? Thank you for your response!