ArticleFrontiers in genetics2015
Trends in substitution models of molecular evolution.
Article in Frontiers in genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 2 of them syntheses that pooled it.
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Who cites it
63 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice.Biological reviews of the Cambridge Philosophical Society · 2026Pooled it
- Phylogenetic congruence, conflict and consilience between molecular and morphological data.BMC ecology and evolution · 2023Pooled it
- Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection.Journal of molecular evolution · 2026Article
- Prion Protein Codon Implicated in Resistance in Dogs Detected in Non-Domesticated Members of Mammalia.Animals : an open access journal from MDPI · 2026Article
- Two new species ofZooKeys · 2026Article
- Evolutionary Tempo, Supertaxa, and Living Fossils.Systematic biology · 2025Article
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning.Molecular biology and evolution · 2025Article
- Accurate prediction of substitution rates at protein sites with a mutation-selection model.Scientific reports · 2025Article
- Article
- Concatenation fails to describe the anomalous radiation of giant cockroaches (Blattodea: Blaberidae) despite moderate to low discordance.BMC ecology and evolution · 2025Article
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Empirical substitution models of protein evolution: database, relationships, and modeling considerations.Database : the journal of biological databases and curation · 2025Article
- Beyond mutations: Accounting for quantitative changes in the analysis of protein evolution.Computational and structural biotechnology journal · 2024Article
- Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept.The protein journal · 2024Article
- Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2024Article
- Substitution Models of Protein Evolution with Selection on Enzymatic Activity.Molecular biology and evolution · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Resolving network clusters disparity based on dissimilarity measurements with nonmetric analysis of variance.iScience · 2023Article
- Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines ineLife · 2023Article
3 more citing papers are in PubMed but not listed here.
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Abstract
Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost 40 years after the development of first substitution models, highly sophisticated, and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis.
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