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. 2022 May 3;23:159. doi: 10.1186/s12859-022-04673-3

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.

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Fig. 6 — We compare KnotAli’s performance using mutual information, $MI$ , versus its performance using adjusted mutual information, $MIp$ . For each family we present the average F-measure obtained when we used (1) MUSCLE as aligner, and $MI$ to find conserved base pairs, presented with MI-MU as the leftmost bar in the figure for each family; (2) MUSCLE as aligner, and $MIp$ to find conserved base pairs, presented with MIp-MU as the second bar from the left in the figure for each family; (3) MAFFT as aligner, and $MI$ to find conserved base pairs, presented with MI-MA as the third bar from the left in the figure for each family; and (4) MAFFT as aligner, and $MIp$ to find conserved base pairs, presented with MIp-MA as the fourth bar from the left in the figure for each family