Dear Dan,

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Thanks

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Yes; but it involves either writing shell scripts (to pipe input into the text-based version of HyPhy), or doing a bit of scripting in the HyPhy batch language. I have quite a few scripts from the time Simon and I were doing simulations for Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login, which may or may not be useful to you. I will be able to give a more helpful answer if you describe the specific workflow you need to automate.

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I am pretty sure it is just the standard dN/dS ratio; where is this parameter reported? If it's not in the paper I linked above, it should have been:)

Cheers,
Sergei

Dear Dan,

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The easiest way to do it is to simply make a text file with all a separate line for each analysis option and the pipe it into HyPhy.

For example include this command in the script presuming that there is a file called "myinfile" with a series of responses to all the prompts that an analysis makes.

`./HYPHYMP CPU=2 < myinfile > /dev/null`

You can make an infile by running HyPhy from the console, and recording the inputs you make. When processing multiple files you could then have a shell script scan the directory for files and substitute input (and output) file names in automatically generates myinfiles. This is klugdy but fast and straightforward.

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Essentially it is indeed an "average" dN/dS estimated using MG94 x whatever model. This parameter is only really meaningful for counting methods, because FEL estimates dN/dS independently for each site, and REL is a separate analysis altogether and estimates the distribution of dN/dS from the data. FEL analyses still estimate average dN/dS but it is merely for reference purposes and not used for inference of selection. User options mean the following:

• Neutral Do not estimate dN/dS, but set it to 1
• User Do not estimate dN/dS, use the value entered by the user
• Estimate dN/dS is estimated from the data along with the tree expansion/contraction factor (as discusses in the paper)
• Estimate+CI Same as previous, PLUS 95% profile likelihood confidence interval is computed for dN/dS
• Estimate dN/dS only dN/dS is estimated from the data along and branch lengths are taken verbatim from an appropriate nucleotide fit. This option is best for FEL, because FEL will compute branch adjustment factors for each site automatically.

HTH,
Sergei

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one more question - does the CPU=2 argument tell HYPHYMP to make use of 2 processors?   Can you set the CPU argument to something less than the total number of processors on a multi-processor machine?

thanks again,
Dan