gubbins 2.3.4-foss-2018b-Python-3.6.6

Deprecated: Use of this version of gubbins is deprecated. More information on our Applications Support and Retention Policy.

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.

Accessing gubbins 2.3.4-foss-2018b-Python-3.6.6

To load the module for gubbins 2.3.4-foss-2018b-Python-3.6.6 please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load gubbins/2.3.4-foss-2018b-Python-3.6.6

BEAR Apps Version




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.


  • reportlab 3.5.21

More Information

For more information visit the gubbins website.


This version of gubbins has a direct dependency on: Biopython/1.72-foss-2018b-Python-3.6.6 DendroPy/4.4.0-foss-2018b-Python-3.6.6 FastTree/2.1.10-foss-2018b foss/2018b Pillow/5.3.0-foss-2018b-Python-3.6.6 Python/3.6.6-foss-2018b RAxML/8.2.12-foss-2018b-hybrid-avx2 zlib/1.2.11-GCCcore-7.3.0

Last modified on 4th June 2019