Figure 3

Phylogenetic relationships of 41 variants of the MLST target that include hctB from Chlamydia trachomatis. (A) Phylogenetic tree based on the MLST target that includes the hctB gene. Each variant of the MLST target is indicated by the allele number and the serotypes in which that variant has been found. The phylogeny has been estimated using Bayesian inferences and rooted using paralog rooting based on the repetitive elements. The numbers on branches are posterior probabilities. The clades discussed in the text have been designated I-V. The repetitive elements found in each MLST variant are illustrated in an alignment to the right (B). The alignment of the repetitive elements is based on the neighbor-joining phylogeny of the element types (C) where the scale bar represents one nucleotide change.