Initial commit

.gitignore

README.md

code/compare_gene_pathogenicity_dynamics.py

code/compile_results.py

code/download_enterobase_assemblies.py

code/iterate_iqtree.py

code/run_ALE.py

code/run_MAD_on_EggNOG_parallel.py

notebooks/01-01-dload_data.ipynb

notebooks/01-02-prepare_trees.ipynb

notebooks/02-01-convert_NCBI_IDs.ipynb

notebooks/02-02-infer_dynamics.ipynb

notebooks/03-compile_outputs.ipynb

notebooks/04-compare_gene_pathogenicity_dynamics.ipynb

...compare_gene_pathogenicity_dynamics.single_copy_ogs.ipynb

notebooks/05-gd_pd_across_genomic_distance.ipynb

notebooks/lib/plot.mplstyle