Hi,

I am working on comparative genomics, and I want to find out the syntenic region of two species. I find there are two kinds of chain files available on UCSC. Is there anyone who knows the difference, and which file should I use to get the syntenic regions?

For instance, the pairwise alignment results between human and chimp are as follows:

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsPanTro5/hg38.panTro5.all.chain.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsPanTro5/reciprocalBest/hg38.panTro5.rbest.chain.gz