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BatchFile for estimate dN/dS per site (Read 1675 times)
Miguel
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BatchFile for estimate dN/dS per site
Aug 21st, 2008 at 6:30pm  
Hi,

I am looking for a BatchFile of Hyphy for estimate dN/dS per site and detect those sites under selection (under a GY94 codon model).
I see that there are several BatchFiles in the Hyphy Package, but I do not know what could be the most interesting for this case.

Thanks,
Miguel  Smiley
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Sergei
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Re: BatchFile for estimate dN/dS per site
Reply #1 - Aug 21st, 2008 at 8:28pm  
Dear Miguel,

If you look at the end of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login you will find a list of TemplateBatchFiles that deal with selection analyses. Hopefully one of them will do what you want.

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Sergei
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Miguel
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Hi Hyphy!

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Re: BatchFile for estimate dN/dS per site
Reply #2 - Sep 8th, 2008 at 11:24am  
Dear Sergei,

Ok, I will use FEL and NielsenYang batch files.
Thanks,

Miguel  Smiley
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Sergei
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Re: BatchFile for estimate dN/dS per site
Reply #3 - Sep 8th, 2008 at 11:28am  
Dear Miguel,

NielsenYang.bf does not account for synonymous rate variation. The best one for REL-type models is PARRIS.bf (tucked under Selection/Recombination).

Cheers,
Sergei
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