Dear Leon,

I did implement the Yang Nielsen (2005 version) branch-site models in the following batch file:

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I checked it on one of the example files in the paper, and the results agreed.
The analysis doesn't do BEB or doesn't directly identify sites under selection, although it does output posterior probabilities of each site's belonging to a given rate class.

Give it a try and let me know what happens.

Cheers,
Sergei

Dear Leon,

Not sure why the RedHat system dies with that error message; let me take a look at the file and get back to you.

Some of the Branch-site models take a [b]really[/b] long time to converge, so  the G4 is probably still chugging away - try to let it finish.

Cheers,
Sergei

Dear Leon,

If you start up the command line version with the -p flag, you'll see a list of post-processing options at the end of an analysis. You may also be able to process previously saved results, if those results are the likelihood function state (complete state, not just an analysis output). Those will be NEXUS files with long HYPHY blocks at the end and are typically written by a 'Save Likelihood Function State' option in the post-processing modules for 'Save Results' or directly by some analyses (e.g. NielsenYang.bf). You can save any likelihood function to a file using the following code in your batch files:

Code:

LIKELIHOOD_FUNCTION_OUTPUT = 7;
fprintf ("file_to_save_to", CLEAR_FILE, likelihood_function_id);

 

In that case you can call
Code:

$HYPHYMP -p savedfile
 

and then use post-processing modules.

YangNielsenBranchSite2005.bf computes posterior probabilities of each site's belonging to a given class, but doesn't save it to a file (instead, a GUI table is opened). You can modify the analysis to write out the matrix 'posteriorMatrix' at the end of the file (or a comma separated version there of), or work on it directly. Alternatively, you can save the likelihood function from YangNielsenBranchSite2005.bf as described above, open it in a GUI version of HyPhy and then use the likelihood parameter table to perform empirical Bayes analyses.

Let me know if this makes sense/helps in any way.

Best,
Sergei