Hi,

I'm wondering if the ancestral state reconstruction methods available in Datamonkey under the ASR module are also implemented/available in HyPhy.

Obviously, they're implemented in HyPhy as Datamonkey uses HyPhy on the backend, etc.  But, I can't find any such analyses under the "Standard Anlyses" menu in the HyPhy GUI, so I can't see what options I need to code a script, etc.  ...I haven't yet looked in the command line...

Thanks,
Dan.

Hi Sergei,

Thanks for the prompt reply.

A simple implementation is actually better than what we're using right now.  Plus, I don't think we could apply the more complex methods to ~14K genes in a reasonable amount of time.

Cheers,
Dan.