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. 2014 Jan 31;15(Suppl 2):S8. doi: 10.1186/1471-2105-15-S2-S8

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Copyright © 2014 Vera-Ruiz et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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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Effect of recoding on phylogenetic estimates. Panel (a) displays the tree that was used to generate alignments of 3000 nucleotides under a time-reversible 4-state Markov model. Panel (b) shows the corresponding tree with edge lengths adjusted according to the RY-recoding scheme. Panel (c) shows the corresponding tree with edge lengths adjusted according to the KM-recoding scheme. Panels (d), (e), and (f) present the corresponding results obtained by analysis of the data generated on the tree in panel (a). The scale bar corresponds to the expected number of substitutions $(i . e ., - \sum_{i = 1}^{4} π_{i} r_{i i})$ .