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. 2019 Aug 19;36(12):2883–2889. doi: 10.1093/molbev/msz182

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© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 1. — Identifying optimal parameters for use with alignment-free. Application of Jensen–Shannon divergence (JSD) and Hellinger Distance (HD) to (A) clear cell renal cell carcinoma (ccRCC) patient RMH004 with a germline sample (GL), multiple samples from the ccRCC tumor (R2-4, R8, R10) and a tumor thrombus from the renal vein (VT) and (B) glioma patient P90 with a germline sample (Normal), multiple samples from the initial grade II glioma (Initials A–F) and two samples from a recurrent grade II glioma (Recur 1A and 1B). (C) A table summarizing branch-score distance (BSD) and symmetric distance (SD) values returned when comparing trees for six patients for which both JSD and HD have been applied. (D) A bar chart summarizing BSD and SD values returned when comparing trees for six patients for which both JSD and HD have been applied. (E) Tree topologies produced using k-mer lengths 13, 15, 17, 19, 21, and 23 in combination with JSD when applying alignment-free methods to patient RMH004. (F) A heatmap representing the BSD between trees produced using varying k-mer lengths and HD applied to patient RMH004. (G) A heatmap representing the BSD between trees produced using varying k-mer lengths and JSD applied to patient RMH004. (H) A line graph representing the BSD between trees produced using increasing k-mer lengths when applying JSD.