These are chat archives for dereneaton/ipyrad
Hi @dereneaton and @isaacovercast , I have a question regarding the ABBA-BABA tests. I used the generate_tests_from_tree function and fixed p3 and p4. Our dataset contains 13 species as ingroup and two outgroup species one is relatively close to the ingroup and the other one is further out. I noticed that the outcome of the tests is quite different depending on which outgroup is selected.
Could you please describe how the loci are selected for the tests?
And what about when individuals of the same clade were pooled together for a test?