gubbins 2.3.4-foss-2018b-Python-3.6.6

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, BEAR Cloud VMs, and CaStLeS VMs):

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

BEAR Apps Version



  • 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