lmc297 / zru_farms

Supplementary data for the ZRU Farms Salmonella project

ZRU Farms Salmonella Project Additional Supplementary Files

Quality Control

multiqc_report.html

Quality control report for trimmed reads and assembled contigs, produced using MultiQC

Salmonella enterica Phylogeny

salmonella_core_ksnp.treefile

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 XMLs/Phylogenies

BEAST 2 XML files and the corresponding within-serotype phylogenies (in Nexus format) reported in the manuscript.

Salmonella Anatum

BEAST 2 XML: anatum_snippy_strict_skyline.xml
Phylogeny (see Figure 5 in the manuscript): anatum_strict_skyline_10burnin_MCC_MEDIANnode_10burninLC_0burninTA.tree

Salmonella Cerro

BEAST 2 XML: cero_snippy_strict_skyline.xml
Phylogeny (see Figure 6 in the manuscript): cerro_strict_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree

Salmonella Kentucky

BEAST 2 XML: kentucky_snippy_relaxed_skyline.xml
Phylogeny (see Figure 7 in the manuscript): kentucky_relaxed_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree

Salmonella Meleagridis

BEAST 2 XML: meleagridis_snippy_strict_skyline.xml
Phylogeny (see Figure 8 in the manuscript): meleagridis_strict_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree

Salmonella Newport

BEAST 2 XML: newport_snippy_relaxed_skyline.xml
Phylogeny (see Figure 9 in the manuscript): newport_relaxed_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree

Salmonella Typhimurium

BEAST 2 XML: typh_snippy_relaxed_skyline.xml
Phylogeny (see Figure 10 in the manuscript): typh_relaxed_skyline_10burnin_MCC_CAnode_10burninLC_0burninTA.tree