122 research outputs found

    simulated data sets

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    Genetic data (*G) and environmental data (*E) infiles that were analyzed in this manuscript. These data sets were simulated in R according to the Wright-Fisher model with selection. Genetic data files with the 'sub' prefix include subsets of individuals and thus have lower sample sizes than the other files (2N = 50 or 100 instead of 200)

    wrapper perl scripts for simulations

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    This compressed directory contains a set of perl scripts that were used to run the R Wright-Fisher simulations and generate the data sets analyzed in this paper

    source code and binaries for spatpg software

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    This compressed directory contains the source C++ code for the software described in the paper. A compiled binary for Linux is also included. An up-to-date version of this software can be downloaded from SourceForge (http://sourceforge.net/projects/spatpg/)

    Model evaluation.

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    <p>Boxplots show the distribution of correlations (Pearson correlation coefficient) between true and inferred ancestry frequencies from each of 10 replicate simulations analyzed with different methods, window sizes (for popanc), generations since admixture, selection regimes, and migration rates.</p

    data sets simulated with quantiNEMO

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    Genetic data (geno*) and environmental data (env*) infiles that were analyzed in this manuscript. These data sets were simulated using quantiNEMO

    perl script to run quantiNEMO simulations

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    This is a wrapper script that I wrote to run quantiNEMO to generate the simulated data files that were analyzed in the paper

    source code and binaries for spatpg software

    No full text
    This compressed directory contains the source C++ code for the software described in the paper. A compiled binary for Linux is also included. An up-to-date version of this software can be downloaded from SourceForge (http://sourceforge.net/projects/spatpg/)

    Performance of methods on simulated data.

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    <p>Results shown for local ancestry frequencies estimates in 20, 50, or 200 generation (gens.) simulations with or without selection or ongoing gene flow and analyzed with the proposed method (popanc) or the HMM in structure: Correlation between true and estimated parameter (correlation), normalized RMSD (CVRMSD), and proportion of cases where the true value was included in the 95% ETPIs (95$ ETPI cov.).</p

    Genetic ancestry in a mouse hybrid zone.

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    <p>Plots show ancestry frequency estimates from three admixed populations. Solid lines in (a-c) give ancestry frequencies along chromosomes for TU, HA, and FS populations. Vertical dotted lines delineate chromosomes and the average ancestry frequency for each chromosome is shown by the dashed, black line. Scatterplots in (e) and (f) depict correlations in ancestry frequencies (relative to the mean for each population) for pairs of populations.</p

    Variation in ancestry frequencies.

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    <p>Boxplots summarize the variance in local ancestry frequencies calculated across 20,002 genetic loci and 10 replicate simulations. This includes 20, 50 and 200 generation simulations without selection, 50 generation simulations with strong or diffuse selection, and 200 generations with low (m = 0.005) or high (m = 0.05) migration.</p
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