Genealogies Unbiased By recomBinations In Nucleotide Sequences

• Introduction
• Installation
  • Required dependencies
  • OSX/Linux - conda
  • Linux - Ubuntu Xenial (16.04) & Debian (unstable)
  • OSX/Linux - from source
  • OSX/Linux/Windows - Virtual Machine
  • Running the tests
• Usage
• License
• Feedback/Issues
• Citation
• Further Information
  • Data from the paper
  • Midpoint rerooting
  • Ancestral sequence reconstruction

Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics. Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used for mitigating the effect of horizontal sequence transfer on phylogenetic reconstructions cannot cope with these new datasets. 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.

Before starting your analysis, please have a look at the Gubbins webpage, manual, tutorial and publication.

Phylogenetic software:

• RAxML
• IQTree
• RAxML-NG
• FastTree
• Rapidnj

Python modules:

• Biopython (>1.59),
• DendroPy (>=4.0)
• Scipy
• Numpy
• Multiprocessing
• Numba

See environment.yml for details. These are in addition to standard build environment tools (e.g. python >=3.8, pip3, make, autoconf, libtool, gcc, check, etc...). There are a number of ways to install Gubbins and details are provided below. If you encounter an issue when installing Gubbins please contact your local system administrator.

Install conda and enable the bioconda channels. This can be done using the normal command line (Linux), with Terminal (OSX) or the Powershell (Windows versions >=10).

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install gubbins

Gubbins has been packaged by the Debian Med team and is trivial to install using apt.

sudo apt-get install gubbins

Install the dependencies and include them in your PATH. Clone or download the source code from GitHub and run the following commands to install Gubbins:

autoreconf -i
./configure [--prefix=$PREFIX]
make
[sudo] make install
cd python
[sudo] python3 -m pip install .

Use sudo to install Gubbins system-wide. If you don't have the permissions, run configure with a prefix to install Gubbins in your home directory.

The easiest way to install the latest version of the code from this repository is to set up a conda environment with the packages needed for installation, then remove gubbins:

conda create -c bioconda -n gubbins_git gubbins python=3.9
conda activate gubbins_git
conda install -c conda-forge libtool autoconf-archive automake pkg-config check pytest
conda remove --force gubbins

Then download and install the repository in the same environment:

git clone https://github.com/nickjcroucher/gubbins
cd gubbins
autoreconf -i
chmod +x configure 
./configure --prefix=$CONDA_PREFIX
make
sudo make install
cd python
python3 -m pip install .

Gubbins can be run through the Powershell in Windows versions >=10. We have also created a virtual machine which has all of the software setup, along with the test datasets from the paper. It is based on Bio-Linux 8. You need to first install VirtualBox, then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.

• ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova

The test can be run from the top level directory:

make check

To run Gubbins with default settings:

run_gubbins.py [FASTA alignment]

Information on on further options can be found in the manual.

Gubbins is free software, licensed under GPLv2.

There is no specific support for development or maintenance of Gubbins. However, we will try to help you out if you report any issues about usage of the software to the issues page.

If you use this software please cite: [Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". doi:10.1093/nar/gku1196, Nucleic Acids Research, 2014.] (http://nar.oxfordjournals.org/content/43/3/e15)

For more information on this software see the Gubbins webpage.

• PMEN1 alignment
• ST239 alignment

From version 1.3.5 (25/6/15) to version 1.4.6 (29/2/16) trees were not midpoint rerooted by default. This doesnt have any effect on the recombination detection, but the output trees may not look as expected. Users are advised to upgrade to the latest version.

From version 3.0.0 onwards, Gubbins will use joint ancestral reconstructions with a modified version of pyjar by default. Version 2 used marginal ancestral reconstruction with RAxML; this is still available in version 3, using the --mar flag (IQtree can also be used for reconstruction in version >3.0.0). This may useful in cases where memory use is limiting. Version 1 used joint ancestral reconstruction with fastML.