Pubmed link: http://www.ncbi.nlm.nih.gov/pubmed/25388108
In this paper we describe all the steps necessary to calculate the dN/dS of all the genes using at least two genomes. We include a brief discussion on assigning orthologs, and of codon-aware alignment of orthologs. We then describe how to use the CODEML program of the PAML package for phylogenetic analysis to calculate the dN/dS and how to perform some statistical tests for positive selection.
A pipeline that is suitable for the analysis described in our paper has been published recently:
Webb et al. (2017), VESPA: Very large-scale Evolutionary and Selective Pressure Analyses.
PeerJ Comput. Sci. 3:e118; DOI 10.7717/peerj-cs.118
More information can be found here:
To download VESPA from GitHub: