GSR: Simulator - Splatche

Basic Package Attributes
AttributeValue
Title Splatche
Short Description Spatial and Temporal Coalescences in Heterogeneous Environment
Long Description SPLATCHE (for SPatiaL And Temporal Coalescences in Heterogenous Environment) is a program that allows to incorporate the influence of environment in the simulation of migration of a given species from one or several origin(s). In a second phase, the molecular genetic diversity of one or several samples drawn from the simulated species can be generated. Geographic area and environmental information have to be specified by the program user in a series of input files. Basically, the virtual world where migrations take place is constituted by a matrix of demes. Each deme has its own environmental characteristics according to the input files. A coalescent-based approach allows to generate the molecular diversity of any population sample. The molecular data obtained can then be analyzed in order to study the signature of the simulated demographic scenario. The goal of this online manual is to describe the technical aspects of the software SPLATCHE (version 1.1). This manual complements the article from Currat, Ray and Excoffier, published in 2004. Further details on the methodology can also be found in Ray (2003) and Currat (2004). The pdf version of the user manual could also be download there.
Version 2.0.1
Project Started 2004
Last Release 8 years, 9 months ago
Homepagehttp://www.splatche.com/
Citations Ray N, Currat M, Foll M, Excoffier L, SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination., Bioinformatics, 12-01-2010 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA,
VariationsBiallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite,
Simulation MethodExact Coalescent,
Input
Data Type
File formatProgram Specific, Other (Ascii raster for geographic map),
Output
Data TypeGenotype or Sequence, Demographic (Population sizes and migrations may be monitored for every demes),
Sequencing Reads
File FormatArlequin, Other (Population sizes and migrations, coalescent distributions may be visualized with bitmap files),
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Logistic Growth, Carrying Capacity (Limited by environment), User Defined (Carrying capacity can be changed at different time),
Gene FlowStepping Stone Models (With even or fixed number of migrants), Island Models (With even or fixed number of migrants), Influenced by Environmental Factors, Admixed Population,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation ModelsStepwise Mutation Model, Heterogeneity among Sites,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Population Events,
Other
InterfaceCommand-line, Graphical User Interface,
Development
Tested PlatformsWindows,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation,

No example publication using Splatche has been provided.

Please propose new citations if you are aware of publications that use this software.


Propose changes to this simulator