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Assumptions of SLAC and REL (Read 2729 times)
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Curious HyPhy user

Posts: 2
Assumptions of SLAC and REL
Oct 18th, 2012 at 5:49am
Dear Hyphy users,

I have just downloaded the Hyphy package and skimmed through the manuals "Getting Started with Hyphy" and "Estimating selection pressures on alignments of coding sequences".

My aim is to test for positive (diversifying) selection in datasets where:
  • I have 10 to 50 sequences of either the same species or different species of the same genus
  • The frequence of recombination is high (tested with seven statistical methods implemented in RDP4)
  • I have single copies of haplotypes (i.e. information about the frequency of haplotypes in the population is discarded)

I have tested for positive selection with PAML and OmegaMap, however, my datasets do not correspond to the assumptions made by the models used in these software (PAML does not take recombination into account and OmegaMap needs information about haplotypes' frequencies).

Would SLAC or REL correspond to my datasets ? Is there something written about the assumptions made by SLAC and REL (I could not find it in the manuals) ?

Best regards,

Maurice Smiley
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Datamonkeys are forever...

Posts: 1658
Gender: male
Re: Assumptions of SLAC and REL
Reply #1 - Oct 26th, 2012 at 8:49am
Hi Maurice,

Use recombination corrected FEL or FUBAR (on data monkey.org). Refer to Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login for details, specifically section 1.6.

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Division of Infectious Diseases
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