Fig. 2: Phylogeny of Maela H. influenzae genomes for 3,970 isolates.
From: Genetic population structure of Haemophilus influenzae at local and global scales
The sample type is indicated by the innermost ring. The phylogeny was estimated using FastTree v.2.1.10 on the core-genome alignment mapped against the H. influenzae reference 86-028NP (NC_007146.2). The 20 largest PopPUNK clusters (>50 isolates) are indicated by coloured dots at the tips of the phylogeny, whereas smaller clusters are in grey. The in silico serotypes (second ring), inferred by using Hicap v.1.0.3, and AMR profiles (eight outer rings), screened with AMRFinderPlus v.4.0.3, are shown by colour as indicated in the legend. An interactive online phylogeny, with additional metadata including cgMLST and cgMLST cluster data, is available at ref. 84.
