title: Measuring Natural Selection.
abstract: In this chapter, I review the basic algorithm underlying the CODEML model implemented in the software package PAML. This is intended as a companion to the software's manual, and a primer to the extensive literature available on CODEML. At the end of this chapter, I hope that you will be able to understand enough of how CODEML operates to plan your own analyses.
authors.affiliation: Microbiological Diagnostic Unit (MDU), Public Health Laboratory, Doherty Institute, 792 Elizabeth St., Melbourne, VIC, 3000, Australia. andersgs@gmail.com.
authors.forename: Anders Gonçalves
authors.initials: AG
authors.lastname: da Silva
mesh_terms: D000465:Algorithms; D003062:Codon / Q000235:genetics; D019143:Evolution, Molecular; D012641:Selection, Genetic / Q000235:genetics*; D012984:Software
chemical_list: D003062:Codon
keywords: Branch models; Branch-Site models; CODEML; Codon substitution model; Natural selection; PAML; Site models; dN/dS ratio