Basic Package Attributes| Attribute | Value |
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| Title | NetRecodon |
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| Short Description | Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography |
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| 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. |
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| Version | 6.0.0 |
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| Project Started | 2012 |
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| Last Release | 7 years, 7 months ago |
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| Homepage | http://code.google.com/p/netrecodon/ |
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| Citations |
Arenas M, Posada D, Coalescent simulation of intracodon recombination., Genetics, Feb. 1, 2010
[Abstract, cited in
PMC
]
|
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| GSR Certification | ✔Accessibility
✔Documentation
Application
Support
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| Last evaluated | June 27, 2019 (189 days ago) |
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Detailed Attributes| Attribute Category | Attribute | | Target | |
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| Type of Simulated Data | Genotype at Genetic Markers,
Diploid DNA Sequence,
Haploid DNA Sequence,
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| Variations | Biallelic Marker,
Single Nucleotide Variation,
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| Simulation Method | Standard Coalescent,
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| Input | |
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| Data Type | Ancestral Sequence,
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| File format | |
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| Output | |
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| Data Type | Genotype or Sequence (Can also simulate genotype of an outgroup (a direct descendant of the root)),
Individual Relationship,
Demographic,
Mutation,
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| Sequencing Reads | |
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| File Format | Fasta or Fastq,
Phylip,
NEXUS,
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| Sample Type | Longitudinal,
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| Phenotype | |
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| Trait Type | |
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| Determinants | |
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| Evolutionary Features | |
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| Demographic | |
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| Population Size Changes | Constant Size,
Exponential Growth or Decline,
Bottleneck (Can also change population size according to user-specified demographic periods),
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| Gene Flow | Island Models,
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| Spatiality | |
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| Life Cycle | |
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| Mating System | |
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| Fecundity | |
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| Natural Selection | |
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| Determinant | |
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| Models | Other (Nonsynonymous synonymous rates ratio dn/ds),
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| Recombination | Uniform,
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| Mutation Models | Markov DNA Evolution Models,
Codon and Amino Acid Models,
Heterogeneity among Sites (Proportion of invariable (do not mutate) sites),
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| Events Allowed | Population Events,
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| Other | |
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| Interface | Command-line,
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| Development | |
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| Tested Platforms | Windows,
Mac OS X,
Linux and Unix,
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| Language | C or C++,
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| License | GNU Public License,
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| GSR Certification | Accessibility,
Documentation,
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No example publication using NetRecodon has been provided.
Please
propose new citations if you are aware of publications that use this software.
