GSR: Simulator - NetRecodon

Basic Package Attributes
AttributeValue
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 8 years, 4 months ago
Homepagehttp://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
Documentation
Application
Support

Last evaluated06-27-2019 (477 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 TypeLongitudinal,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Bottleneck (Can also 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 NetRecodon has been provided.

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