Browsing a Gingr file

  • 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
  • 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)