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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> Bayesian network analysis on large dataset http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1359044376 Message started by Catherine Macken on Jan 24^th, 2013 at 8:19am

Title: Bayesian network analysis on large dataset
Post by Catherine Macken on Jan 24^th, 2013 at 8:19am

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.

Title: Re: Bayesian network analysis on large dataset
Post by Sergei on Jan 24^th, 2013 at 8:32am

Hi Catherine,

I would suggest that you refer to Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login section 1.8 which has a tutorial on how to run BGM analyses in HyPhy.
Also make sure you get a fairly recent HyPhy version -- there was a period when HyPhy BGM files were broken in the distribution.

Sergei

Title: Re: Bayesian network analysis on large dataset
Post by Catherine Macken on Jan 25^th, 2013 at 7:57am

Thanks. I look forward to my adventure. Catherine

Title: Re: Bayesian network analysis on large dataset
Post by Art F. Poon on May 16^th, 2013 at 12:10am

Hi Catherine,
Sorry I haven't replied to your post - my account on the board got deleted and I had a lot of trouble trying to get a new one set up. I wrote the Bayesian network code and would be happy to help you with your analysis.
Cheers,
- Art.

Title: Re: Bayesian network analysis on large dataset
Post by Jason on Sep 21^st, 2013 at 6:52am

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

Title: Re: Bayesian network analysis on large dataset
Post by daven on Oct 1^st, 2013 at 9:26pm

Hi all,
I am also using the most recent hyphy-2.2 version and I get exactly the same error message as Jason, both with an installation of the program on a linux server and on my own macbook pro.

Any help will be greatly appreciated, I have tried a thousand things and always ended up getting the same error message.

Thanks in advance :)