Maximum Likelihood Tree — IQ-TREE2 (GTR+G, 1000 ultrafast bootstrap) on Parsnp core-genome SNPs
Color by
Layout
Bootstrap
Bootstrap circles: ● ≥95
● 70–94
● 50–69
(hidden if <50)
Sample Details
Click a node on the tree
to view sample details
to view sample details
Antimicrobial Resistance Gene Matrix — Abricate / CARD (≥90% identity, ≥80% coverage)
Sample Collection Timeline by Hospital
Pairwise SNP Distance Matrix (IQ-TREE ML distances × 4 Mb genome)
Colour scale: white = 0 SNPs → deep red = many SNPs. Click a cell to compare two samples.
cgMLST Allele Distance Matrix — Pasteur schema · 2390 loci · chewBBACA 3.5.3
0–10 alleles (same cluster)
11–50
>50
Red border = ≤10 allele pairs (outbreak threshold)
SNP vs cgMLST Allele Distance — Concordance
Each point = one isolate pair shared between both matrices. Pearson r shown in corner.