Code

The programs developed during the project are hosted in this project. Each program file contains instruction for users and/or developers. Use cases of individual programs are introduced in Protocols.

No installation is required. Each script or notebook should work out-of-the-box, with or without a few common dependencies. To simplify usage, we recommend using conda to create a virtual Python environment to host dependencies:

conda create -n wol -c conda-forge python=3 scikit-bio scikit-learn seaborn biom-format
source activate wol

• scripts: Python scripts.

• notebooks: Jupyter Notebooks.

• utils: Python modules used by scripts and notebooks.

• prototypeSelection: Algorithms for “prototype selection”, a statistical process that is central to the genome sampling process of this project.

Some utilities developed during this work have been merged into the latest releases of scikit-bio, an integrated Python package for bioinformatics.