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HYPHY Package >> HyPhy feedback >> sites under positive selection http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1308178731 Message started by fabia on Jun 15th, 2011 at 3:58pm |
Title: sites under positive selection Post by fabia on Jun 15th, 2011 at 3:58pm
Hi Sergei,
I am trying to identify sites under positive selection in a set of sequences that I simulated. The simulation was run so that all sites and all branches have an omega=1 (therefore, no sites should be detected as being under positive selection). I ran this data set in PamL (model 0, nsites 2) and, as expected, no sites were found under positive selection. In HyPhy, I am using dNdSRateAnalysis.bf followed by dNdSResultProcessor.bf as shown in the exercise on the InfluenzaA_H3_Random35 example. Using a BF threshold of 50 I find 827 codons (total number of codons is 1000) under positive selection. Am I doing something wrong or is there a reason for why HyPhy finds positive selection where there shouldn't be and where PamL doesn't find it? Thanks, fabia A partial example of my final output: Counter Site Index Log[BF{NS/S>1|s}] 1 1 5.38119 2 2 7.41881 3 3 7.12305 4 4 9.64254 5 7 6.73498 |
Title: Re: sites under positive selection Post by Sergei on Jun 15th, 2011 at 4:22pm
Hi Fabia
Can you post the alignment that gave the odd results? Sergei |
Title: Re: sites under positive selection Post by fabia on Jun 16th, 2011 at 10:11am
Mhmm, I am trying but it gives me an error. I sent it directly to your email.
Fabia |
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