Query regarding PAML

[Manisha Ghosh]

Hi,

Recently in one of my manuscript where I mentioned about PAML for evolutionary rate estimation. 

I have written "The evolutionary rates of each genes from each taxonomic (with reference to consensus sequence) were calculated using Codeml program included in the PAML software package (ver. 4.5) (Nei and Gojobori 1986, Yang 2007) (http://abacus.gene.ucl.ac.uk/software/paml.html) with runmode = −2 and CodonFreq = 1." 

Reviewer commented " PAML is not run in a standard model testing phylogenetic mode." 

There have been some confusion because I mentioned PAML Codeml program for evolutionary rate estimation not for any phylogenetic model testing. Please let me know whether my thinking is correct and how should I convince reviewer about my explanation.

Thank you all

Manisha Ghosh