ArticleBMC bioinformatics2007
Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
- New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2.Briefings in bioinformatics · 2021Article
- Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients.Genes · 2018Review
- Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses.PloS one · 2018Article
- The Bacterial Sequential Markov Coalescent.Genetics · 2017Article
- Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.PLoS computational biology · 2016Article
- SimBac: simulation of whole bacterial genomes with homologous recombination.Microbial genomics · 2016Article
- A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups.Evolutionary bioinformatics online · 2015Article
- 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
- πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.BMC bioinformatics · 2014Article
- Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.Molecular biology and evolution · 2014Article
- Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences.BMC bioinformatics · 2014Article
- Protein evolution along phylogenetic histories under structurally constrained substitution models.Bioinformatics (Oxford, England) · 2013Article
- How good are indirect tests at detecting recombination in human mtDNA?G3 (Bethesda, Md.) · 2013Article
- Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection.BMC microbiology · 2013Article
- Computer programs and methodologies for the simulation of DNA sequence data with recombination.Frontiers in genetics · 2013Article
- Simulation of molecular data under diverse evolutionary scenarios.PLoS computational biology · 2012Article
- Detection of recombination events in bacterial genomes from large population samples.Nucleic acids research · 2012Article
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2 authors.
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Abstract
backgroundCoalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences sampled from populations with recombination, migration and growth.
resultsWe introduce a new coalescent program, called Recodon, which is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general time-reversible model of nucleotide substitution with a proportion of invariable sites and among-site rate variation. In addition, the program implements non-reversible processes and mixtures of different codon models.
conclusionRecodon is a flexible tool for the simulation of coding DNA sequences under realistic evolutionary models. These simulations can be used to build parameter distributions for testing evolutionary hypotheses using experimental data. Recodon is written in C, can run in parallel, and is freely available from http://darwin.uvigo.es/.
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