Beginners guide to caclulating dN/dS

Published on (GMT) by Daniel Jeffares
Pubmed link: http://www.ncbi.nlm.nih.gov/pubmed/25388108 Journal: http://dx.doi.org/10.1007/978-1-4939-1438-8_4 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: http://mol-evol.org/VESPA To download VESPA from GitHub: https://github.com/aewebb80/VESPA
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