ArticleMolecular biology and evolution2014
Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.Communications biology · 2026Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- Evaluation of haplotype callers for next-generation sequencing of viruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination.BMC bioinformatics · 2020Article
- Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients.Genes · 2018Review
- Microbial sequence typing in the genomic era.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- TreeToReads - a pipeline for simulating raw reads from phylogenies.BMC bioinformatics · 2017Article
- Article
- SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.Systematic biology · 2016Article
- SimBac: simulation of whole bacterial genomes with homologous recombination.Microbial genomics · 2016Article
- CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.Molecular biology and evolution · 2015Article
- Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.Journal of molecular evolution · 2015Article
- Article
- Trends in substitution models of molecular evolution.Frontiers in genetics · 2015Article
- Spatial and temporal simulation of human evolution. Methods, frameworks and applications.Current genomics · 2014Article
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2 authors.
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Abstract
Genomic evolution can be highly heterogeneous. Here, we introduce a new framework to simulate genome-wide sequence evolution under a variety of substitution models that may change along the genome and the phylogeny, following complex multispecies coalescent histories that can include recombination, demographics, longitudinal sampling, population subdivision/species history, and migration. A key aspect of our simulation strategy is that the heterogeneity of the whole evolutionary process can be parameterized according to statistical prior distributions specified by the user. We used this framework to carry out a study of the impact of variable codon frequencies across genomic regions on the estimation of the genome-wide nonsynonymous/synonymous ratio. We found that both variable codon frequencies across genes and rate variation among sites and regions can lead to severe underestimation of the global dN/dS values. The program SGWE-Simulation of Genome-Wide Evolution-is freely available from http://code.google.com/p/sgwe-project/, including extensive documentation and detailed examples.
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