Bioinformatics. 2019 Nov 1;35(21):4480-4483. doi: 10.1093/bioinformatics/btz311.

SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.

Currat M^1,², Arenas M^3,⁴, Quilodràn CS¹, Excoffier L^5,⁶, Ray N^7,⁸.

Author information

1: Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland.
2: Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva 1211, Switzerland.
3: Department of Biochemistry, Genetics and Immunology, Vigo 36310, Spain.
4: Biomedical Research Center (CINBIO), University of Vigo, Vigo 36310, Spain.
5: Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland.
6: Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
7: Institute of Global Health, GeoHealth Group, University of Geneva, Geneva 1205, Switzerland.
8: Institute for Environmental Sciences, University of Geneva, Geneva 1205, Switzerland.

Abstract

SUMMARY:

SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework. The new capabilities include long-distance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a large variety of DNA mutation models. These implementations have been applied independently to various studies, but grouped together in the current version.

AVAILABILITY AND IMPLEMENTATION:

SPLATCHE3 is written in C++ and is freely available for non-commercial use from the website http://www.splatche.com/splatche3. It includes console versions for Linux, MacOs and Windows and a user-friendly GUI for Windows, as well as detailed documentation and ready-to-use examples.