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. 2016 Sep 27;17:397. doi: 10.1186/s12859-016-1167-6

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© The Author(s). 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 2 — Iterative solutions of integral equation system for local PWA probabilities. The results shown in this figure apply to both case (ii) and case (iii) local PWAs. In both panels, the abscissa is the number of sites between PASs (i.e., ∆L ^A for case (ii) and ∆L ^D for case (iii)), with zero corresponding to case (i). Each panel shows the ratio of the total contribution from histories with up to (and including) N _ID indels to the “exact solution” of the multiplication factor. See section M1 of Methods for the parameter setting. Panel a is for 0.04 expected indels per site, and panel b is for 0.2 expected indels per site. Panels a and b in this figure are modified versions of panels B and C, respectively, of Figure 3 of [43]