How does Mega do it?  Is there a special build and if so is it freely available (along with a list of allowable function calls etc)?  Alternatively, has anyone had any luck running/compiling a command line version of hyphy in MS windows?

Hi Darren,

Yes, there is a special version (which is included in the downloadable source; you should be able to compile the LIB target using make LIB after you have called CMake; I am not sure how this will work with your Windows environment because I haven't tried it myself.

Essentially you compile it as a DLL and then have a few high level calls available to you (look at the source of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login)

Alternatively, you can compile HyPhy on Windows using CygWin (or minGW) as a Linux compatibility layer.

MEGA is currently calling HyPhy as a binary (via named pipes).

You can download the version I compiled for the MEGA folks last year from here: Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Sergei