HyPhy message board
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
Datamonkey Server >> Datamonkey feedback >> REL, FEL, IFEL selected amino acid residues
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1379942840

Message started by Men on Sep 23rd, 2013 at 6:27am

Title: REL, FEL, IFEL selected amino acid residues
Post by Men on 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?

Title: Re: REL, FEL, IFEL selected amino acid residues
Post by Sergei on 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

Title: Re: REL, FEL, IFEL selected amino acid residues
Post by Men on Sep 26th, 2013 at 9:22am
Hello Sergei,

Thanks for the clarification

HyPhy message board » Powered by YaBB 2.5.2!
YaBB Forum Software © 2000-2023. All Rights Reserved.