KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
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Summary
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.
- Type
- article
- Published
- 2007-05-23
- Cited by
- 1,094
- References
- 37
- Access
- Open access
- OpenAlex
- https://openalex.org/W2003062832
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:9614433
Keywords
Calculator, Model selection, Selection (genetic algorithm), Computer science, Artificial intelligence
References
- A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.
- Evolution of the Zfx and Zfy genes: rates and interdependence between the genes.
- PAML: a program package for phylogenetic analysis by maximum likelihood
- Some probabilistic and statistical problems in the analysis of DNA sequences
- A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
- Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
- A codon-based model of nucleotide substitution for protein-coding DNA sequences.
- Unbiased estimation of the rates of synonymous and nonsynonymous substitution
- Estimation of evolutionary distances between nucleotide sequences
- Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
- Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates
- Estimation of evolutionary distances between homologous nucleotide sequences.
- The neutral theory of molecular evolution.
- Model Selection and the Molecular Clock
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
- MODELTEST: testing the model of DNA substitution
- K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals
- Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.
- Evolutionary trees from DNA sequences: A maximum likelihood approach
- Estimation of evolutionary distance between nucleotide sequences.
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- Accelerated Evolution of Fetuin Family Proteins in Protobothrops flavoviridis (Habu Snake) Serum and the Discovery of an L1-Like Genomic Element in the Intronic Sequence of a Fetuin-Encoding Gene
- High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake
- A 454 sequencing approach to dipteran mitochondrial genome research.
- The rubber tree genome reveals new insights into rubber production and species adaptation
- Unexpected but welcome. Artificially selected traits may increase fitness in wild boar
- Population structure and local selection yield high genomic variation in Mimulus guttatus
- High genetic diversities between isolates of the fish parasite Cryptocaryon irritans (Ciliophora) suggest multiple cryptic species.
- Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification
- A Genomic Survey of Angiotensin-Converting Enzymes Provides Novel Insights into Their Molecular Evolution in Vertebrates
- Mitochondrial genomes and their utility for the recovery of phylogeny in the Hymenoptera
- Genetic variation within the Daphnia pulex genome
- Positively selected genes of the Chinese tree shrew (Tupaia belangeri chinensis) locomotion system.
- [Molecular evolution of the poplar MIR169 gene family].
- Multigene phylogenetic analyses to delimit new species in fungal plant pathogens.
- Phylogénie, éléments transposables et évolution de la taille des génomes chez les lupins
- Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats
- Identyfikacja domen WG/GW zaangażowanych w wiązanie białek Argonaute oraz analiza mechanizmów molekularnych odpowiedzialnych za ich zmienność
- Genome-wide survey and expression analysis of the PUB family in Chinese cabbage (Brassica rapa ssp. pekinesis)
- Genetic variation in the FMO2 gene: evolution & functional consequences
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