Distance computation outside MicrobeTrace : SeqRuler
https://github.com/Sergey-Knyazev/SeqRuler
This is a tool with a simple GUI to calculate TN93 distances between sequences in your dataset if you have a large dataset with either many or very long sequences (e.g. SARS-CoV-2). This tool helps compute distances quickly to give you an edge list which can be used as input into MicrobeTrace to visualize genetic distance networks.
Note that the tool ignores ambiguities.
- Select Load Fasta (sequences **MUST **be aligned), enter the threshold value of your choice. Edges with distances above the cut-off value will not be included in the final output
- Specify the file name and location of your output edge list (output will be in the form of a .csv file)
- Select Run TN93
Once it is complete, you can open the edge list file. Below is an example.
This edge list can now be loaded into MicrobeTrace along with related metadata.