Additional file 6: Figure S3. of Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia

Core genome phylogenies of Group II strains. A) Core genome phylogeny of C. botulinum Group II strains inferred with RAxML [63] using the ASC_GTRGAMMA model on an alignment of 200,276 core genome SNPs produced with NASP [61] using C. botulinum strain Alaska E43 [GenBank:CP001078] as the reference. The consistency index is 0.81, and the retention index is 0.90 (computed with the R package phangorn). B) Core genome phylogeny of Group II C. botulinum strains inferred with FastTree2 [54] on a 35,382-character core SNP matrix generated with kSNP [59]. The consistency index is 0.83, and the retention index is 0.90. The phylogenies were rooted with the clade that includes strains Eklund 202F, KAPB-3, Eklund 17B and CDC 66177. Gray circles indicate bootstrap values over 95 %. While there are small variations in the phylogenies generated with different methods (Fig. 6 and Additional file 6: Figure S3), Group II strains are separated into two distinct clades. The pairwise overall topological scores computed by Compare2Trees [69] range from 93 to 100 %. (PDF 35 kb)