Codeml parameter set-up.

[Szabi Kormány]

Hey everyone! I recently downloaded pamlX on my computer to detect positive and/or negative selection for around 40 BRCA1 sequences as it's part of my undergrad dissertation. First, I'm trying to detect selection in each animal groups (rodents, cetaceans etc.) then all of them together. When it comes to setting up the parameters, I'm a bit confused of what means what. I was trying to use the Branch-site model first but it says "Error: dN/dS ratios among branches not implemented for gamma." Can someone explain me what this means exactly? And also how to set up the parameters to get valid information out of them? Help would be very much appreciated. 

[Sandra AC]

Hi there,

As far as I am concerned, pamlX is not maintained anymore, and this issue might be related to package incompatibilities in new operating systems. Running all PAML programs from the terminal is the best way to ensure best performance :) 

In addition, you can follow our latest protocol, Beginner's Guide on the Use of PAML to Detect Positive Selection, which hopefully will help you understand how to run CODEML from the terminal under various models implemented in the program. Note that you can clone our GitHub repository `positive-selection` to reproduce all the analyses we go through in the protocol -- we even include a section explaining how we parsed the raw data!

Hope this helps!
S.