I am a VERY newbie HyPhy user, and so perhaps this is plunging in the deep end too quickly. However, I would like to infer a Bayesian network for a dataset that exceeds the limits allowed by datamonkey.org. Is there a batch file available for this process? Or perhaps a command line file? (I have a good tree already.) I use a Mac G5 desktop, and have installed HyPhy, which recognizes that my desktop has multiple processors. I also may have access to a cluster that uses MPI, on which I may be able to install and run HyPhy.  I would appreciate your suggestions.

Thanks.  I look forward to my adventure.  Catherine

Hello Art and Sergei,

I too am trying to run a BGM analysis. I downloaded and started using HyPhy only last week and so my version should be the most up-to-date. I have been going through the Epistasis section 1.8 in  Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login to get a feel for the tool. I have used all the default parameter settings (and tried some others) and get the following error after choosing ancestral resampling (both yes and no):

Error: The left hand side expression does not contain an object reference in the following context: 'BGM gen_bgm=<ERROR HERE>(discreteNodes.continuou'

Function call stack
1 : BGM gen_bgm=(discreteNodes,continuousNodes)

Any help/guidance you can give would be greatly appreciated.

Thanks,
Jason