GSR: Simulator - Recodon
Attribute | Value |
---|---|
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 | 15 years, 2 months ago |
Homepage | https://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 |
Last evaluated | 03-12-2020 (1472 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, |
Variations | Biallelic Marker, Single Nucleotide Variation, |
Simulation Method | Standard Coalescent, |
Input | |
Data Type | Ancestral Sequence, |
File format | |
Output | |
Data Type | Genotype or Sequence (Can also simulate genotype of an outgroup (a direct descendant of the root)), Individual Relationship, Demographic, Mutation, |
Sequencing Reads | |
File Format | Fasta or Fastq, Phylip, NEXUS, |
Sample Type | |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck (Change population size according to user-specified demographic periods), |
Gene Flow | Island Models, |
Spatiality | |
Life Cycle | |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | |
Models | Other (Nonsynonymous synonymous rates ratio dn/ds), |
Recombination | Uniform, |
Mutation Models | Markov DNA Evolution Models, Codon and Amino Acid Models, Heterogeneity among Sites (Proportion of invariable (do not mutate) sites), |
Events Allowed | Population Events, |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using Recodon has been provided.
Please propose new citations if you are aware of publications that use this software.