Dear Sergei,
This alignment contains 30 sequences of 333 codons, and many codons are PSS.
The links with the results are:
- FEL (0.1 significance level):Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
- FEL (0.2 significance level): Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
- REL (50 significance level): Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
- REL (40 significance level): Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
- SLAC (0.1 significance level): Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
- SLAC (0.2 significance level): Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
First, SLAC have found a very few PSS, even at 0.2 significance level, so I think, I am going to elimate this option.
FEL detects many PSS and REL detects also several PSS (not so many as FEL). When I change the significance level (in FEL to 0.2 and in REL to 40) I can see that FEL find more (and quite correctly) not positive selection sites and PSS than REL. The sites predicted by REL were also quite correctly detected.
So, I have to choose between FEL and REL. Looking to the problems of convergence in M7 and M8 models of NielsenYang.bf, what method do you think could be better for this case?
Thans for your help!
Cheers,
Miguel