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. 2017 Jan 5;18:19. doi: 10.1186/s12864-016-3407-6

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© The Author(s). 2017

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. 3 — Phylogenetic tree inferred by CSI phylogeny. This is the un collapsed version of the best scoring tree according to the new method for tree comparison. The phylogeny is inferred by CSI Phylogeny on all 101 sequenced strains, using the assembled contigs from the root strain as reference genome, SNP pruning disabled