Initial commit

.gitignore

README.md

code/analyse_hyphy_output.py

code/compare_gene_ecosystem_dynamics.py

code/compile_results.py

code/download_eggnog_ncbi_genome_assemblies.py

code/download_ncbi_genome_sequences.py

code/iterate_iqtree.py

code/prepare_nog_nucl_seqs.py

code/run_ALE.py

code/run_MAD_on_EggNOG_parallel.py

code/run_hyphy_parallel.py

mamba_packages.yml

notebooks/01-01_download_data.ipynb

notebooks/01-02_find_eggnog_gold_overlap.ipynb

...ooks/01-03_prepare_subset_of_genes_trees_alignments.ipynb

notebooks/01-04_prepare_genome_tree.ipynb

notebooks/02-infer_GD_ED.ipynb

notebooks/03-compile_outputs.ipynb

notebooks/04-compare_gene_ecosystem_dynamics.ipynb