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

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.

SUPPLEMENTARY INFORMATION

Details about the implemented evolutionary models and parameters are provided in the software documentation available at http://www.splatche.com/splatche3.

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  • Publisher Full Text
  • Authors+Show Affiliations

    ,

    Laboratory of anthropology, genetics and peopling history, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland. Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.

    ,

    Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain. Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.

    ,

    Laboratory of anthropology, genetics and peopling history, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.

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    Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. Swiss Institute of Bioinformatics, Lausanne, Switzerland.

    Institute of Global Health, GeoHealth group, University of Geneva, Geneva, Switzerland. Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland.

    Source

    Pub Type(s)

    Journal Article

    Language

    eng

    PubMed ID

    31077292

    Citation

    Currat, Mathias, et al. "SPLATCHE3: Simulation of Serial Genetic Data Under Spatially Explicit Evolutionary Scenarios Including Long-distance Dispersal." Bioinformatics (Oxford, England), 2019.
    Currat M, Arenas M, Quilodran CS, et al. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics. 2019.
    Currat, M., Arenas, M., Quilodran, C. S., Excoffier, L., & Ray, N. (2019). SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics (Oxford, England), doi:10.1093/bioinformatics/btz311.
    Currat M, et al. SPLATCHE3: Simulation of Serial Genetic Data Under Spatially Explicit Evolutionary Scenarios Including Long-distance Dispersal. Bioinformatics. 2019 May 11; PubMed PMID: 31077292.
    * Article titles in AMA citation format should be in sentence-case
    TY - JOUR T1 - SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. AU - Currat,Mathias, AU - Arenas,Miguel, AU - Quilodran,Claudio S, AU - Excoffier,Laurent, AU - Ray,Nicolas, Y1 - 2019/05/11/ PY - 2019/01/22/received PY - 2019/04/18/revised PY - 2019/04/19/accepted PY - 2019/5/12/entrez JF - Bioinformatics (Oxford, England) JO - Bioinformatics N2 - 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. SUPPLEMENTARY INFORMATION: Details about the implemented evolutionary models and parameters are provided in the software documentation available at http://www.splatche.com/splatche3. SN - 1367-4811 UR - https://www.unboundmedicine.com/medline/citation/31077292/SPLATCHE3:_simulation_of_serial_genetic_data_under_spatially_explicit_evolutionary_scenarios_including_long-distance_dispersal L2 - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btz311 DB - PRIME DP - Unbound Medicine ER -