Figure 1

Maximum-likelihood phylogenies based on whole genome and SNP concatenated sequence alignment. Phylogenetic trees based on whole genome sequences (a), SNP concatemers using CS as reference (b) and SNP concatemers using the H37Rv genome sequence as reference (c) were constructed using PhyML 3.0 [39]. Most probable trees were selected based on aLTR statics implemented in PhyML [39]. Isolates, clustered into different positions compared with the phylogenetic tree based on the whole genome sequences of M. tuberculosis strains RGTB327 and RGTB423, are indicated in the squares. For the KZN series, inversion-corrected sequences were used for the alignment and marked “_m”. aLTR statics values for each branch are shown. In Figure 1a, clusters of lineage 4 and 2 are indicated in the squares.