All external software/package dependencies are checked at the beginning of the workflow, and if given user permission, will download automatically prior to running. Please note that Python must be version 3.5 or higher to avoid the need for backwards compatibility.
Links to repositories used:
prokka: https://github.com/tseemann/prokka
RGI: https://github.com/arpcard/rgi
Bioconda: https://github.com/bioconda
IQ-TREE: https://github.com/Cibiv/IQ-TREE
ete3: https://github.com/etetoolkit/ete
DendroPy: https://github.com/jeetsukumaran/DendroPy
.
├── config
├── docs
│ └── pipeline_visualization.png
├── README.md
├── requirements.txt
├── scripts
│ ├── pipeline_prototype2.sh
│ ├── pipeline_protoype1.sh
│ └── pipeline.sh
├── setup.py
├── test
└── workflow
├── envs
│ └── gene_neighborhoods_pipeline.yml
└── scripts
├── make_ML_tree_vis.py
├── __pycache__
│ └── make_ML_tree_vis.cpython-38.pyc
├── tree_clustering.py
└── tree_distances.pyJulia Lewandowski @ (JTL-lab)