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 and BEAR Cloud VMs):

📋 module load bear-apps/2022a
module load Gubbins/3.3.1-foss-2022a

BEAR Apps Version

2022a

Architectures

EL8-cascadelake — EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

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