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Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography
1Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310 Vigo, Spain. miguelab@uvigo.es
BMC Bioinformatics
|November 22, 2007
Summary
Recodon is a new coalescent program that simulates coding DNA sequences. It models complex evolutionary scenarios, including recombination, migration, and demography, for robust population genetics research.
Area of Science:
- Population Genetics
- Molecular Evolution
- Bioinformatics
Background:
- Coalescent simulations are vital for population genetics.
- Accurate simulations require realistic molecular evolution models.
- Existing coalescent programs lack the ability to simulate codon sequences with multiple evolutionary forces.
Purpose of the Study:
- Introduce Recodon, a novel coalescent program.
- Enable simulation of coding DNA sequences under complex evolutionary scenarios.
- Integrate multiple evolutionary forces like recombination, migration, and demography.
Main Methods:
- Developed a coalescent program named Recodon.
- Implemented an extended general time-reversible codon model.
- Incorporated features for non-reversible processes and model mixtures.
Main Results:
- Recodon simulates coding DNA sequences with interacting evolutionary forces.
- The program supports recombination, migration, and demographic changes.
- It includes advanced nucleotide substitution models with rate variation.
Conclusions:
- Recodon is a versatile tool for simulating coding DNA sequences.
- Facilitates the creation of parameter distributions for hypothesis testing.
- Provides a flexible platform for realistic evolutionary modeling in population genetics.
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