i´m analyzing two genomes (Genome 1 and Genome 2) and i have pair genes from those two related species. I want to know if the positive selection happened.
For this, i want to use the Branch test in codeml to test the significance of the analysis determining the maximum likelihood ratio with the following hypothesis:
Ho: one ratio (model 0, fix_omega 0, neutral)
H1: free ratio (model 1, Fix_omega 1, variation)
but i´m not sure if it is the appropriate method to identify genes that are statistically under positive selection in my pairwise comparison.
I know that for pairwise comparison i have to use model -2, but i don´t know how to test the hypothesis under this runmode value.
So the questions are : 1.Are the parameters for testing the hypothesis good? or How can I set them? 2.In order to validate my hypothesis using runmode -2, How can I set the parameters now in the control file?
for that reason, I would like to know your opinion about it.