NCBI

BLAST

Multiple sequence alignment

Figure 1

Alignments shown in seaview

Figure 2

Alignments shown in seaview

Phylogenetics

Figure 1

Manually built UPGMA tree
UPGMA tree

Figure 2

Reads, QC and trimming

Figure 1

Schematic workflow of the bioinformatics workflow

Figure 2

Quality control workflow

Figure 3

A FastQC output showing reads with good quality

Figure 4

A FastQC output showing reads with bad quality

Sequence assembly

Mapping

Figure 1

Mapping of SNP reads

Figure 2

Figtree
As shown by FigTree

Figure 3

phylo.io
As shown by phylo.io, stable version

Figure 4

beta.phylo.io
As shown by phylo.io, beta version. Note the position of the “99”

Molecular epidemiology

Figure 1

workflow