Has anybody tried Phylogenetic Analysis by Maximum Likelihood (PAML) in Windows.
How to calculate omega for many bacteria of same species to check positive selection?
I didn't get it through their manual.
What commands should be given through cmd.
You need to read the section "Downloading and Setting up PAML" and then subsection "Windows 9x/NT/2000/XP/Vista/7"
This info may be missing from the manual, so have a go at looking through this stuff if you've not tried it already.
Note that there is no "program" called "paml" or "PAML", rather you run individual programs within the PAML packaged (in your case it would be codeml)
I've never used PAML under windows, but I think the idea is the same as under *nix i.e. the instructions about which data file to use, and which paramenters to run the analysis with, are specified in a "control" file that you set up (and give an appropriate name to) prior to running the programs