Fig. 1

Presence and absence of marker genes in the training dataset. The phylogenetic tree is based on the alignment of 455 core genes (present in at least 90% of the strains) inferred from 215 whole genome sequencing datasets of human-related Haemophilus spp. A Presence/absence of marker genes that specifically discriminate between H. haemolyticus and H. influenzae. B Presence/Absence of haemin biosynthesis genes (hem*), which are colored according to the species identity of the reference alleles for which a valid hit was found. C Presence/absence of lacZ, a β-galactosidase gene that differentiates between H. parahaemolyticus and H. paraphrohaemolyticus. D Presence/absence of nadV, which is related to the H. ducreyi characteristic V factor independency. E Presence/absence of Region I (bex*), region II and region III (hcs*) capsule loci (in silico serotyping). All annotated Haemophilus spp. clades were separated with a strong local support value (100%)