Table 1 Congruency parameters between phylogenomic reconstructions of strains belonging to different serovars of Salmonella enterica subsp. enterica (n = 440) in terms of distance and topology. The phylogenomic reconstructions were performed by maximum likelihood selecting the most appropriate models of evolution and checking ultrafast bootstrap convergences (i.e. IQ-Tree). The compared approaches ‘variants’ and ‘genes’ correspond to phylogenomic trees reconstructed using pseudogenomes from variant calling analysis (i.e. iVARCall2) including (A) or excluding (B) variants from recombination events (i.e. ClonalFrameML), and concatenated orthologous genes (C) from pangenome analysis (i.e. Roary), respectively. The cophenetic function of the ‘dendextend’ R package was used to compute the cophenetic correlations. The dendrogram function of the ‘dendextend’ R package was used to compute the Fowlkes-Mallows indexes. The treedist function of the ‘phangorn’ R package was used to compute the Robinson-Foulds indexes

From: Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale