Initial commit

.gitignore

01-prepare_data/01-01-prepare_NOG_dataset_dload_seqs.ipynb

01-prepare_data/01-02-prepare_nucleotide_data.ipynb

01-prepare_data/src/download_ncbi_genome_sequences.py

01-prepare_data/src/run_MAD_on_EggNOG_parallel.py

02-run_programs/02-run_programs.ipynb

02-run_programs/program_runs

02-run_programs/src/FC_analysis.py

02-run_programs/src/angst_penalty_file.txt

02-run_programs/src/run_ALE.py

02-run_programs/src/run_Wn.py

02-run_programs/src/run_angst.py

02-run_programs/src/run_rangerdtl.py

03-analyse_outputs/03-01-compile_results.ipynb

03-analyse_outputs/03-02-cotransfer_analyses.ipynb

03-analyse_outputs/03-03-intersections.ipynb

...yse_outputs/03-04-function_vs_acquisitions_analyses.ipynb

...utputs/03-05-coacquisitions_by_gene_characteristics.ipynb

03-analyse_outputs/compiled_results

03-analyse_outputs/lib/coacq_logscale_summary_lib.py