I've been looking at tools to predict variant effects in non-human organisms (other mammalian species). I'm aware of polyphen-2 and SIFT, and really need a tool/tools that can be downloaded and installed locally to run the service on large batches of data. I've read scattered information about standalone polyphen-2, but it seems that I cannot find definite instructions or documentations about how you set this up. Plus, the pre-built databases on polyphen-2 website cannot be downloaded anymore (http://genetics.bwh.harvard.edu/pph2/dokuwiki/downloads). Anyone has some experiences to run polyphen-2 locally on a non-human species? Any advice would be really helpful!