Quality control report for trimmed reads and assembled contigs, produced using MultiQC
Phylogeny constructed using core SNPs identified among 570 Salmonella enterica genomes using kSNP3/IQ-TREE, in Nexus format (see Figure 1 in the manuscript)
BEAST 2 XML files and the corresponding within-serotype phylogenies (in Nexus format) reported in the manuscript.
BEAST 2 XML: anatum_snippy_strict_skyline.xml
Phylogeny (see Figure 5 in the manuscript): anatum_strict_skyline_10burnin_MCC_MEDIANnode_10burninLC_0burninTA.tree
BEAST 2 XML: cero_snippy_strict_skyline.xml
Phylogeny (see Figure 6 in the manuscript): cerro_strict_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree
BEAST 2 XML: kentucky_snippy_relaxed_skyline.xml
Phylogeny (see Figure 7 in the manuscript): kentucky_relaxed_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree
BEAST 2 XML: meleagridis_snippy_strict_skyline.xml
Phylogeny (see Figure 8 in the manuscript): meleagridis_strict_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree
BEAST 2 XML: newport_snippy_relaxed_skyline.xml
Phylogeny (see Figure 9 in the manuscript): newport_relaxed_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree
BEAST 2 XML: typh_snippy_relaxed_skyline.xml
Phylogeny (see Figure 10 in the manuscript): typh_relaxed_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree