Fig. 5
From: Comparative genomics of whole-cell pertussis vaccine strains from India
Phylogenetic analysis of vaccine and clinical strains using cgMLST. Maximum-likelihood phylogenetic tree for Indian Bordetella pertussis isolates and vaccine strains and isolates from other geographical origins based on concatenated alignments of 2038 cgMLST gene sequences. The tree was rooted with strain Bordetella parapertussis (GenBank Accession number CP019931.1). Tree scale is indicated above the diagram. The external circle indicates the geographical origin of isolates (blue, France; red, India; Pink, Vermont; Green, UK; Yellow, California; Orange, Washington; Purple, Michigan). Vaccine strains and Indian Isolates labels highlighted in bold red colour. The scale bar indicated amino-acid substitution per site. The tree was constructed with bootstrap values 1000 replicates. Bootstrap values are indicated with the position on branch 50 and scale by factor 1