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XOrigin is a pipeline to estimate expansion origins from derived SNPs, which incorporate temporal and spatial heterogeneity. It is best suited for estimating refugia for species that experienced distributional shifts during last glacial maximum. The pipeline is dependent on SPLATCHE2 for spatially-explicit demographic simulations, and make use o…
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README.md

X-ORGIN

XOrigin is a pipeline designed for estimating expansion origins from derived SNPs, which incorporates temporal and spatial heterogeneities. It is best suited for estimating refugia for species that experienced distributional shifts during last glacial maximum. The pipeline is dependent on SPLATCHE2 for spatially-explicit demographic simulations, and makes use of the spatial statistics Psi to estimate expansion origins.

To cite, please include the following papers:

Qixin He, Joyce Padro, L. Lacey Knowles. (2017 in press) Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program X-ORIGIN. Mol. Ecol.

Peter, Benjamin M., and Montgomery Slatkin. “Detecting Range Expansions from Genetic Data.” Evolution 67, no. 11 (November 1, 2013): 3274–89. doi:10.1111/evo.12202.

Nicolas Ray, Mathias Currat, Matthieu Foll, and Laurent Excoffier. “SPLATCHE2: A Spatially Explicit Simulation Framework for Complex Demography, Genetic Admixture and Recombination.” Bioinformatics 26, no. 23 (December 1, 2010): 2993–94. doi:10.1093/bioinformatics/btq579.

Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander, and Laurent Excoffier. “ABCtoolbox: A Versatile Toolkit for Approximate Bayesian Computations.” BMC Bioinformatics 11 (2010): 116. doi:10.1186/1471-2105-11-116.

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