An official website of the United States government
GSR: Simulator - Splatche
| Attribute | Value |
|---|---|
| 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 | 13 years, 3 months ago |
| Homepage | http://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, Dec. 1, 2010 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Sept. 28, 2022 (896 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite |
| Simulation Method | Exact Coalescent |
| Input | |
| Data Type | |
| File format | Program Specific, Other (Ascii raster for geographic map) |
| Output | |
| Data Type | Genotype or Sequence, Demographic (Population sizes and migrations may be monitored for every demes) |
| Sequencing Reads | |
| File Format | Arlequin, Other (Population sizes and migrations, coalescent distributions may be visualized with bitmap files) |
| Sample Type | Random or Independent |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Logistic Growth, Carrying Capacity (Limited by environment), User Defined (Carrying capacity can be changed at different time) |
| Gene Flow | Stepping 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 System | Random Mating |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | Stepwise Mutation Model, Heterogeneity among Sites |
| Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events |
| Other | |
| Interface | Command-line, Graphical User Interface |
| Development | |
| Tested Platforms | Windows |
| Language | C or C++ |
| License | GNU Public License |
| GSR Certification | Documentation, Application |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used Splatche.
2022
Larsson DJ, Pan D, Schneeweiss GM, Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling., Alp Bot, Jan. 1, 2022 [Abstract]
Silva NM, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, et al., Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis., Sci Rep, Aug. 5, 2022 [Abstract]