Distance computation outside MicrobeTrace : SeqRuler
https://github.com/cdcgov/seqruler?tab=readme-ov-file
This is a tool with a simple GUI to calculate TN93 or SNP distances between sequences in your dataset if you have a large dataset where sequences are either too many or too long (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.
The tool has multiple options to process 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 OR Run SNP
- Select how you would like to process the ambiguities if using TN93
- Select number of cores to use
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.