├── .github ├── dependabot.yml └── workflows │ ├── docker-publish.yml │ ├── run-testdataset.yml │ └── upload-release.yml ├── Dockerfile ├── LICENSE.txt ├── README.md ├── edgehog ├── __init__.py ├── add_ons.py ├── characterize_species_tree.py ├── check_args.py ├── edgehog.py ├── hdf5.py ├── infer_ancestral_synteny_graphs.py ├── init_extant_synteny_graphs.py ├── process_hogs.py ├── read_gff.py └── write_output.py ├── pyproject.toml ├── test_data ├── FastOMA_HOGs.orthoxml ├── README.md ├── gff3 │ ├── CALJA.gff │ ├── CHLSB.gff │ ├── GORGO.gff │ ├── HUMAN.gff │ ├── MACFA.gff │ ├── MACMU.gff │ ├── NOMLE.gff │ ├── PANPA.gff │ ├── PANTR.gff │ ├── PAPAN.gff │ └── PONAB.gff ├── sequences.tgz └── species_tree.nwk └── utils └── extract_age_timetree.py /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DessimozLab/edgehog/HEAD/.github/dependabot.yml 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