Gubbins 3.3.1-foss-2022a

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, 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.

Accessing Gubbins 3.3.1-foss-2022a

To load the module for Gubbins 3.3.1-foss-2022a please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load Gubbins/3.3.1-foss-2022a

BEAR Apps Version

2019b

More Information

For more information visit the Gubbins website.

Dependencies

This version of Gubbins has a direct dependency on: Biopython/1.79-foss-2022a DendroPy/4.5.2-GCCcore-11.3.0 FastTree/2.1.11-GCCcore-11.3.0 foss/2022a IQ-TREE/2.2.2.6-gompi-2022a numba/0.56.4-foss-2022a Python/3.10.4-GCCcore-11.3.0 rapidNJ/2.3.3-GCCcore-11.3.0 RAxML/8.2.12-gompi-2022a-avx2 RAxML-NG/1.1.0-GCC-11.3.0 SciPy-bundle/2022.05-foss-2022a SKA2/0.3.4-GCCcore-11.3.0

Last modified on 6th November 2023