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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. 6 — Simulation analyses on absolute alignment frequencies. Each panel compares the predicted absolute frequency of each local homology structure (ordinate) against the number of times that it actually occurred in a simulated dataset (abscissa). The predicted absolute frequency was calculated using Eq. (SM-7.1) in Additional file 1. Note the logarithmic scaling for both axes, which tends to exaggerate sampling errors on the lower-left region in each panel. Panels a, b and c, respectively, show the results with the simulated sets 1A, 1B and set 1B after removing long gapped segments. The panels a-c are reformatted versions of panels A-C of Figure 29 of [48]