Hi,

I am very new at phylogenies analysis and using HyPhy; so, I apologise in advance for the naivety (and possible non-sense) of my questions.

I need to analise if some residues in a set of proteins are evolving under positive/negative selection. I aligned the cDNAs and generated the trees. As I have few sequences per alignment, I am using REL (dBdSRateAnalysis.bf). After that, I saw that I can select positively selected codons using dNdSResultProcessor.bf but I couldn't find any template to determine the negatively selected codons.

In addition, I am not sure of understanding correctly the output. Is Log[BF{NS/S>1|s}] the ln of the Bayes Factor? Is this number the same as P[NS/S>1|s]? Could I use P[NS/S<=1|s] to find the negatively selected codons?

Many thanks.

David  

Dear Sergei,

Thanks for your answer.

I continue on having problems with understanding the output (probably due to my lack of statistical expertise). I have used the flu example to do some tests. I observed that the Log[BF{NS/S>1|s}] value of the positively selected sites is the same as their P[NS/S>1|s]. As you said that the former is the natural logarithm of the Bayes Factor, whereas the other is the Posterior Probability (used to calculate the BF), shouldn't this values be different?

Sorry for the naivety of my questions.

Best,
David

Dear Sergei,

I included all the options in the attached .bf file. I used the Flu alignment from your website and I inferred the tree using HyPhy.

This is a detail of the output when using "Positive Selection":
Codon      P[NS/S>1|s]      P[NS/S<=1|s]
1      0      2.51214
2      0      1.73459
3      1.57905      0
4      0      2.08207
5      0      1.71434
6      0      1.35117
7      0      1.35117
8      5.05474      0
9      0      1.85867

This is a detail of the output when using "Find Positively Selected Sites":
Counter      Site Index      Log[BF{NS/S>1|s}]
1      8      5.05474
2      10      4.40309
3      11      8.00546
4      12      4.29289
5      21      4.75764
6      69      7.70401
7      100      7.58658
8      102      7.84679
9      110      4.54851

When running the same dataset on datamonkey, I got slightly different results in terms of selected positions (I suppose that the options are not the same I used in HyPhy). Looking at the HTML report, I see that all posterior probabilities are <= 1 and that P{dN>dS}+P{dN<dS} = 1. Finally, Bayes Factors are different to posterior probabilities.

Many thanks for your help.

Cheers,
David

Dear Sergei.

Then, can I assume that the other column (P[NS/S<=1|s]) is the ln(BF) of being negatively selected? Is this right or I am wrong?

All the best,
David