Basic Package AttributesAttribute | 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 | 6 years, 8 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 |
This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.
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Detailed AttributesAttribute 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 | |
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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.