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GSR: Simulator - NetRecodon
| Attribute | Value |
|---|---|
| Title | NetRecodon |
| Short Description | Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography |
| Long Description | NetRecodon is a population genetic simulator that generates samples of nucleotide and codon sequences from haploid/diploid populations with inter and intracodon recombination, migration, growth and dated tips. It can also run in several processors using MPI. Operative systems Source code and a makefile are provided for compilation in any OS with a C compiler, along with some compiled executables. |
| Version | 6.0.0 |
| Project Started | 2012 |
| Last Release | 11 years, 10 months ago |
| Homepage | http://code.google.com/p/netrecodon/ |
| Citations | Arenas M, Posada D, Coalescent simulation of intracodon recombination., Genetics, 02-01-2010 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 06-27-2019 (1752 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 | Longitudinal, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck (Can also 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 NetRecodon has been provided.
Please propose new citations if you are aware of publications that use this software.