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. 2022 Feb 17;12:803190. doi: 10.3389/fmicb.2021.803190

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Copyright © 2022 Guang, Howison, Ledingham, D’Antuono, Chan, Lawrence, Dunn and Kantor.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Multi-dimensional scaling (MDS) of pairwise geodesic distance among maximum-likelihood phylogenies from the profile sampling approach within genomic regions. MDS Axis 1 (X axis) and Axis 2 (Y axis) show that the space of inferred phylogenies is multi-modal for all genomic regions. The phylogenies from NGS and Sanger consensus sequences (dot and triangle) are point estimates that do not capture the full variation in phylogenies that can be inferred from deeply-sequenced NGS data (plus signs) in all examined genomic regions (colors).