phage PIN and aging simulation

first principle simulation of phage PIN: Can I regenerate the exponetial survival curves?

J Virol. 2013 Dec;87(23):12745-55. doi: 10.1128/JVI.02495-13. Epub 2013 Sep 18.

The protein interaction network of bacteriophage lambda with its host, Escherichia coli.

Blasche S1, Wuchty S, Rajagopala SV, Uetz P.

https://www.ncbi.nlm.nih.gov/pubmed/24049175

BMC Microbiol. 2011 Sep 26;11:213. doi: 10.1186/1471-2180-11-213.

The protein interaction map of bacteriophage lambda.

Rajagopala SV¹, Casjens S, Uetz P.

https://www.ncbi.nlm.nih.gov/pubmed/21943085

codeml on polymorphism data

  Question: codeml on polymorphism data for selection?? treating polymorphism as divergence? Using codeml on multiple genome data is common. Is this an abuse of codeml?