run_gubbins
phylogenetic analysis of genome sequences
Install
- All systems
-
curl cmd.cat/run_gubbins.sh
- Debian
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apt-get install gubbins - Ubuntu
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apt-get install gubbins - Kali Linux
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apt-get install gubbins - Windows (WSL2)
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sudo apt-get updatesudo apt-get install gubbins - Dockerfile
- dockerfile.run/run_gubbins
gubbins
phylogenetic analysis of genome sequences
Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.