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. 2014 May 15;10(5):e1004342. doi: 10.1371/journal.pgen.1004342

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© 2014 Rasmussen et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) Recovery of global features of simulated ARGs from sequence data. This plot is based on sets of 20 1-Mb sequences generated under our standard simulation parameters (see Methods) with (see Supplementary Figure 10 for additional results). From left to right are shown true (-axis) versus inferred (-axis) values of the log joint probability (the logarithm of equation 2), the total number of recombinations, and the total branch length of the ARG. Each data point in each plot represents one of 100 simulated data sets. In the vertical dimension, circles represent averages across 100 sampled ARGs based on the corresponding data sets, sampled at intervals of 10 after a burn-in of 200 iterations, and error bars represent the interval between the 2.5 and 97.5 percentiles. In the second and third plots, circles are interpretable as posterior expected values and error bars as 95% Bayesian credible intervals. (B) Posterior mean TMRCA (dark red line, with 95% credible intervals in light red) versus true TMRCA (black line) along a simulated genomic segment of 1 Mb. This plot is based on a single representative data set of 20 1-Mb sequences generated under our standard simulation parameters with (see Supplementary Figure S5 for additional results).

Inline graphic — (A) Recovery of global features of simulated ARGs from sequence data. This plot is based on sets of 20 1-Mb sequences generated under our standard simulation parameters (see Methods) with (see Supplementary Figure 10 for additional results). From left to right are shown true (-axis) versus inferred (-axis) values of the log joint probability (the logarithm of equation 2), the total number of recombinations, and the total branch length of the ARG. Each data point in each plot represents one of 100 simulated data sets. In the vertical dimension, circles represent averages across 100 sampled ARGs based on the corresponding data sets, sampled at intervals of 10 after a burn-in of 200 iterations, and error bars represent the interval between the 2.5 and 97.5 percentiles. In the second and third plots, circles are interpretable as posterior expected values and error bars as 95% Bayesian credible intervals. (B) Posterior mean TMRCA (dark red line, with 95% credible intervals in light red) versus true TMRCA (black line) along a simulated genomic segment of 1 Mb. This plot is based on a single representative data set of 20 1-Mb sequences generated under our standard simulation parameters with (see Supplementary Figure S5 for additional results).