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REL, FEL, IFEL selected amino acid residues (Read 4249 times)
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REL, FEL, IFEL selected amino acid residues
Sep 23rd, 2013 at 6:27am
 
Hello,

I am running SLAC, IFEL, REL to find codons within my alignment that are under positive selection.  I have observed that datamonkey only shows the codons that are selected and not the particular amino acid resisues that are being selected for.  I used to see the selected amino acid residues in datamonkey when I was running the analyses about 2 months ago but now I don't see them anymore. Can someone please let me know how to see the selected amino acid residues?
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Sergei
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Re: REL, FEL, IFEL selected amino acid residues
Reply #1 - Sep 25th, 2013 at 11:07am
 
Hi there,

Other than PRIME, TOGGLE and DEPS/FADE, other datamonkey methods do not report specific residues subject to selection, just the sites. Can you be more specific about what you were able to see 2 months ago that you can no longer see? If you are referring to the ability to view inferred substitutions at a specific site, this information is based on SLAC results only (however MEME also report similar information using a different model), and you should be able to access these links from the Integrative link on the Analysis Information page.

Sergei
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Re: REL, FEL, IFEL selected amino acid residues
Reply #2 - Sep 26th, 2013 at 9:22am
 
Hello Sergei,

Thanks for the clarification
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