Skip to main content
Fig. 2 | BMC Microbiology

Fig. 2

From: First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts

Fig. 2

Phylogenetic inference based on coregenome single nucleotide polymorphisms (SNPs) identified in Salmonella enterica subsp. enterica serovars Dublin, Enteritidis, Pullorum, and Gallinarum. The color legend corresponds to serovars presented by Langridge et al. (Proc. Natl. Acad. Sci. 2015;112:863–8). The variants were identified by the ‘VARCall’ workflow against the reference genome S. Enteritidis (strain P125109, accession NC_011294.1). The produced pseudogenomes (4,685,848 bp) were inferred with RAxML based on a bootstrap analysis and search for best-scoring Maximum Likelihood tree with General Time-Reversible model of substitution and the secondary structure 16-state model. Bootstraps higher than 90% are represented by black circles. The phylogenetic inference converged after 200 bootstrap replicates with a log likelihood score of −8.106 for 1000 computed trees. The tree is rooted on the branch of S. Dublin

Back to article page