Main tool: Gubbins
Code repository: https://github.com/nickjcroucher/gubbins
Basic information on how to use this tool:
- executable: run_gubbins.py
- help: -h
- version: --version
- description: Gubbins detects recombinations through the locally elevated densities of polymorphisms that arise when sequence segments are acquired from a donor genetically divergent from the set of analyzed sequences.
Full documentation: https://github.com/nickjcroucher/gubbins/blob/master/docs/gubbins_manual.md
run_gubbins.py fasta_alignment.aln