gubbins 2.3.4-foss-2018b-Python-3.6.6

Unsupported: Use of this version of gubbins is not supported. 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, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps-unsupported/handbuilt/2019
module load gubbins/2.3.4-foss-2018b-Python-3.6.6

BEAR Apps Version

2019h

Extensions

  • reportlab 3.5.21

More Information

For more information visit the gubbins website.

Dependencies

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