Fig. 1
From: Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan
Maximum likelihood reconstruction of whole genome phylogeny of ocular Chlamydia trachomatis sequences from Sudan. Whole genome and plasmid phylogeny of 12 C. trachomatis sequences from Sudan and 188 Ct clinical and reference strains. Sudanese C. trachomatis sequences were mapped to C. trachomatis A/HAR-13 using Bowtie2. SNPs were called using SAMtools/BCFtools. Phylogenies were computed with RAxML from a variable sites alignment using a GTR + gamma model and are midpoint rooted. The scale-bar indicates evolutionary distance. Sudanese C. trachomatis sequences generated in the present study are coloured green, and reference strains are coloured by tissue localization (blue, ocular; yellow, urogenital; purple, LGV)