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. 2014 Nov 12;14:591. doi: 10.1186/s12879-014-0591-3

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© Christiansen et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. 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 use, distribution, and reproduction in any medium, provided the original work is properly credited. 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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Neighbour-joining reconstruction of the phylogeny of C. trachomatis . The figure shows an un-rooted phylogenetic reconstruction of the alignment data including 8 cultured and 8 clinical C. trachomatis samples sequenced in this study and 23 C. trachomatis genomes obtained from GenBank. The Neighbour-joining tree was constructed with 500 bootstrap replicates using a Jukes Cantor model of evolution and gamma correction for among-site rate variation with four rate categories. The gap/missing data was treated with a site coverage cut-off of 90%. The blue clusters represent the ocular/urogenital biovar (dark blue T2 clade and light blue T1 clade) and the red cluster represents the LGV biovar. The ocular serovars A-C cluster within the dark blue T2 clade. The samples sequenced in this study are highlighted in colours (blue and red) and the GenBank strains are represented in black.