NetRecodon

Basic Package Attributes
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	7 years ago
Homepage	http://code.google.com/p/netrecodon/
Citations	Arenas M, Posada D, Coalescent simulation of intracodon recombination., Genetics, Feb. 1, 2010 [Abstract, cited in PMC ]
GSR Certification	This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification .

Detailed Attributes
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