├── .eggs └── README.txt ├── .gitignore ├── MANIFEST.in ├── README.md ├── data └── nodesdb.gz ├── dist └── kinfin-0.9-py2.7.egg ├── example ├── OrthologousGroups.txt ├── SequenceIDs.txt ├── SpeciesIDs.txt ├── config.txt ├── fasta │ ├── A.proteins.faa │ ├── B.proteins.faa │ ├── C.proteins.faa │ ├── D.proteins.faa │ ├── E.proteins.faa │ └── F.proteins.faa ├── functional_annotation.txt ├── interproscan.tsv └── tree.nwk ├── install ├── kinfin ├── license.md ├── requirements.txt ├── scripts ├── __init__.py ├── filter_fastas_before_clustering.py ├── filter_isoforms_based_on_gff3.py ├── filter_sequences_from_blast.py ├── filter_sequences_from_clustering.py ├── functional_annotation_of_clusters.py ├── generate_kinfin_input.py ├── generate_network.py ├── get_count_matrix.py ├── get_protein_ids_from_cluster.py ├── iprs2table.py └── plot_cluster_size_distribution.py ├── setup.cfg ├── setup.py ├── src ├── __init__.py └── kinfin.py └── test /.eggs/README.txt: 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