I'm wanting to test for selection on a set of aligned genes, and codeml looked like a good place to start. The program EasyCodeML (https://github.com/BioEasy/EasyCodeML) is a wrapper for the core codeml program, but the Github distribution is very vague on how to actually install it and get it to run.
Currently, the EasyCodeML-master file is in my Documents. I was able to find the .jar file easily, but when I try to launch it from Finder, it gives two errors. The first one says 'Can't found 'codeml.exe' or 'chi2.exe', and the second one says 'Could NOT found the Custom Files in the same directory of EasyCodeML.jar.'
There are a set of chi2.exe and codeml.exe files in a folder labeled 'Mac', and I assume I need to do something to install the program, but I''m confused as to what that is. Any help would be appreciated.