├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── conda ├── build.sh ├── conda_upload.sh └── meta.yaml ├── eden ├── __init__.py ├── align │ └── __init__.py ├── display │ ├── __init__.py │ └── graph_layout.py ├── graph.py ├── io │ ├── __init__.py │ ├── gspan.py │ ├── node_link_data.py │ ├── sequence.py │ └── word_sequence.py ├── iterated_maximum_subarray.py ├── ml │ ├── __init__.py │ ├── estimator.py │ ├── estimator_utils.py │ ├── link_prediction.py │ ├── link_prediction_utils.py │ └── ml.py ├── sequence.py └── util.py ├── git-revision.sh ├── requirements.txt ├── requirements2.txt ├── requirements3.txt ├── resources ├── EDeN_logo.png ├── EDeN_logo.svg ├── EDeN_logo_small.png └── example_restart_python.py ├── setup.py └── test ├── __init__.py └── disabled_tests ├── test_annotate_cycle.py ├── test_annotate_rna_secondary_structure.py ├── test_eden_modifier_graph_vertex_attributes.py ├── test_fasta_to_sequence.fa ├── test_fasta_to_sequence.py ├── 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