Recent, I had read one paper :https://academic.oup.com/nar/article/40/22/11463/1147721. In this paper, the author identified hundreds of conserved non-coding genomic regions that were independently lost in mammals. It is very interesting. But, I want to know how do extract hundreds of CNEs (conserved non-coding element) loss events from whole-genome multiple alignment files (MAF) in specific-lineage.

Is there have some software or scripts can do it.

Thanks.