title: KaKs_Calculator: calculating Ka and Ks through model selection and model averaging.
abstract: KaKs_Calculator is a software package that calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. Since existing methods for this estimation adopt their specific mutation (substitution) models that consider different evolutionary features, leading to diverse estimates, KaKs_Calculator implements a set of candidate models in a maximum likelihood framework and adopts the Akaike information criterion to measure fitness between models and data, aiming to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into this software.
authors.affiliation: Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China.
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Xiao-Qian
authors.initials: XQ
authors.lastname: Zhao
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution; D019143:Evolution, Molecular; D008962:Models, Theoretical; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012984:Software
chemical_list: D011506:Proteins