I had 11 primates gene and to know branch specific selection procedure i used aBSERLin Datamonkey.org. But data showing, w=10^9 some show two omega parameter..i align the sequences from clustal omega codon alignment and then remove stop from it. then perform aBSERL.
1-Can anyone tell me what I'm doing wrong.
2- or how i can interpret results from data monkey server?
3-can anyone guide me through it??
10^9 is, as you point out an absurd number. So large that it suggests that convergence of the parameter estimates is not happening. It cannot return infinity (no convergence) so it returns an impossibly large number instead. The data are not amendable, perhaps, to selections analysis.
If mine does not seem like an adequate explanation, pleas don't hesitate to provide more details of the analysis. I have done a great deal of selection analysis using HyPhy and DataMonkey (same packages one on computer, one online)
I'm extremely sorry for that.
i'm working with 11 primates species and 1st I draw a MLE tree then my task was to know branch specific Ka/Ks..for that I perform absrel from datamoneky.org and results ware showing like this in my attached log file...for macaca fasicularis web result shows value showed two omega value and one of these was 10^9..
1)i can able to interpret this data like why two omega value..
2)what are those percentages mean in log file.
3)i want to know about all 3 types of selection, which one is occurring or not?
4) can you suggest me any other web server or tool to know branch specific Ka/Ks??
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