Hello:

I am trying to use the methods of Lemey, et al. to calculate mean synonymous and nonsynonymous substitution rates for time-structured sequence data. It appears that the script Prof. Lemey's script dNdSFixedLength.bf does not work with the gui version of HyPhy. It isn't obvious to me how I can get a command-line version of HyPhy. Do I need to download the source code and recompile? Is there a command-line-only executable for Mac?

Thanks for your help with this.

Kurt Wollenberg

Hi Kurt,

You can always build a command line version of HyPhy using OS X developer tools and cmake (which is a build system that you may need to install separately -- it's free), using the links and README from the HyPhy development page Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

However, you may find it easier to use the batch file from Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login to repeat the analyses we did for the Lemey et al paper. dNdSFixedLengths.bf was an internal file not meant for public distribution.

Best,
Sergei

Hi Sergei:

Thanks for this. It seemed to be running well for me but then threw an error about operation "MAccess". I've attached a screen shot of the error message including the status at the bottom of the HyPhy window in case that helps.

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Hi Kurt,

Can you look in the about box and see which version of HyPhy you are using? The batch files are quite old, so it is entirely possible that the current version of HyPhy complains about them. I'll see if I can fix them. Did you run the file on the example included in the archive?

Also, when you click on OK in the error box, you should see more messages -- the one about MAccess is a generic error about trying to access an element in something which is not a matrix or dictionary.

Sergei

Hi Sergei:

When I first tried to run the batch file it quit because it didn't like the version of HyPhy that was installed. I went to the site and got the latest version and used that. I didn't try the example files, I just jumped right in with my data.

There were more error messages once I clicked through. I've attached screen shots of these (compressed into an archive).

Thanks for the quick response on this.
Cheers,
Kurt

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Hi Sergei:

I also got the same errors with the example data.

Cheers,
Kurt

Hi Kurt,

I found the bug -- I think we only used the version of the script for MPI for the paper, and you were trying to run it on a desktop (serially). Should work if you redownload  Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and run CodonFitter once again.

Sergei

Hi Sergei:

CodonFitter is humming along. Thanks very much for this!

Cheers,
Kurt