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, BEAR Cloud VMs, and CaStLeS 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.
- BlueBEAR: The OS used on BlueBEAR 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.
- BEAR Cloud and CaStLeS VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
- reportlab 3.5.21
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