faircloth-lab/phyluce — comment on commit 87f9b0276c3a0470b7c5db452aaf6b3246aa6649
File: phyluce/helpers.py line 69
By brantfaircloth:

Prior to this change, we were penalizing for fewer matches than expected, which is very likely a "normal" outcome rather than the result of a duplication event. We're still filtering to ensure matches are on the same chromosome and within physical range of one another.