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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Datamonkey Server >> Datamonkey feedback >> selection at internal branches vs tips http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1273555397 Message started by Lauro on May 10^th, 2010 at 10:23pm

Title: selection at internal branches vs tips
Post by Lauro on May 10^th, 2010 at 10:23pm

Dear Art and Sergei,

I have a couple of questions,
1.- what is meaning of just find codons positively selected at internal branches by IFEL, but not by other methods like SLAC or FEL and REL.

2,.using gabranch, what is the difference of finding the positive selection at tips versus internal branches.

My best
Lauro.

Title: Re: selection at internal branches vs tips
Post by Sergei on May 12^th, 2010 at 6:39pm

Hi Lauro,

1). At those sites, diversifying selection is limited to interior branches, while (likely) purifying selection took place at the tips. Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login for an example from the world of HIV

2). I am not sure I follow your question: GA-branch does not treat tips vs internal branches differently. Also GA-branch assumes that dN/dS is the same for all sites.

Sergei