Dear Dr. Sergei Kosakovsky Pond,

I have two questions when analysing data on DataMonkey server:

(1). I run FEL/IFEL on DataMonkey server. But, "Addditional Information" column is missing on the positive selected sites table (the results page). Browsers I used are IE 7.0 and Safari

(2). How to choose P values : 0.05? (based on the paper "Adaption to Different Human Populations by HIV-1 Revealed by codon-Based Analyses")

Thanks!

Ben

Dear Ben,

It is not explicitly documented, but you need to have SLAC results for the additional information column to be generated; run SLAC first (to get ancestral sequences and such) and then FEL/IFEL. I will update the documentation to reflect this - thanks for pointing out this issue.

As far as p-values go: use 0.05 if you have > 50-70 sequences and 0.1 for fewer sequences. FEL/IFEL are conservative for smaller alignments so the nominal value of p=0.1 will actually result in lower false positives; at least that's the case in all the simulations we have done.

Cheers,
Sergei

Dear Sergei,

Thank you very much! I will do it as you suggested!  

One more question:

I want to compare two populations in terms of positive selection sites. Based on your paper "Adaptation to different human populations by HIV-1 revealved by codon-based analysis", you identified six codons in RT (82, 98, 165, 177, 196, and 202) as selected differentially in the two populations at p< 0.05 (see Table 2).  my questoin is the calculation of "Different" on table 2 can be done on DataMonkey server? If yes, how to...  If not, any suggestion?

Thanks!

Ben

Dear Sergei,

I am still waiting for your response! I have two populations with 70 sequences for each one. I try to test if these two populations are selected differentially at P < 0.05. Can I do this on DataMonkey server. If not, what is suggestion?

In fact, I check PyPhy package, and  find "compareSelectivePressureIVL.bf" under a standard analysis. But, I can't find instruction for how to do it!

Thanks!

Ben

Dear Ben,

Datamonkey.org does not handle the comparison analysis, but HyPhy does. Please examine section 2.7.1 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for detailed instructions of how to do this.

Best,
Sergei

thanks Gergei!

Ben