Main tool: Gubbins
Code repository: https://github.com/nickjcroucher/gubbins
Additional tools:
- RAxML: 8.2.12
- FastTree: 2.1.11
- IQTree: 2.0.3
- RAxML-NG: 1.0.1
- Rapidnj: 2.3.2
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