Beginners guide to caclulating dN/dS

Published on by Daniel Jeffares
Pubmed link: Journal: 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. Software: 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:

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