GSR: Simulator - Recodon

Basic Package Attributes
AttributeValue
Title Recodon
Short Description Coalescent simulation of coding DNA sequences with recombination, migration and demography
Long Description Recodon can 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.
Version 1.6.0
Project Started 2009
Last Release 11 years, 9 months ago
Homepagehttps://github.com/MiguelArenas/recodon
Citations Arenas M, Posada D, Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography., BMC Bioinformatics, 11-20-2007 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated03-12-2020 (218 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodStandard Coalescent,
Input
Data TypeAncestral Sequence,
File format
Output
Data TypeGenotype or Sequence (Can also simulate genotype of an outgroup (a direct descendant of the root)), Individual Relationship, Demographic, Mutation,
Sequencing Reads
File FormatFasta or Fastq, Phylip, NEXUS,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Bottleneck (Change population size according to user-specified demographic periods),
Gene FlowIsland Models,
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
ModelsOther (Nonsynonymous synonymous rates ratio dn/ds),
RecombinationUniform,
Mutation ModelsMarkov DNA Evolution Models, Codon and Amino Acid Models, Heterogeneity among Sites (Proportion of invariable (do not mutate) sites),
Events AllowedPopulation Events,
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using Recodon has been provided.

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