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
- 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)