Quickstart

Browsing a Gingr file

• Download Gingr input file
• Open in Gingr (File->Open)

• The phylogeny appears on the left. Hover over a clade to highlight and outline the corresponding tracks to the right.

• Click to zoom in on the clade

• The multiple alignment appears on the right, shown as a SNP heatmap when zoomed out. To see the full alignment, zoom in with the mouse wheel or by selecting a region in the ruler.

Importing other files

• Create a new workspace (File->New)

• Download the data files
  • Alignment: xmfa
  • Reference: fasta
  • Annotations: genbank
  • Phylogeny: newick
• Import the alignment with the refrence (File->Import Alignment (XMFA & Fasta))

• The track highlighted in blue (“england.gbk.fna.srt”) is the current reference for variants. Select a new reference by right-clicking on a track.

• Next, import the phylogenetic tree (File->Import tree (Newick))

• Reroot the tree at the midpoint (Tree->Reroot at midpoint)

• The tree will now be balanced at the center of the longest path

• Finally, import the annotations (File->Import annotations (Genbank))

• The workspace can be saved to share or return to later (File->Save)