{ "info": { "author": "Violeta Beleva Guthrie", "author_email": "vbeleva@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "NAPA - Network Analysis of Protein Adaptation\n---------------------------------------------\n\nThe NAPA package performs intra-protein residue coevolution network construction and analysis.\n\nThe package supports two input types: \n\n1. A FASTA alignment of (functionally related) homologous protein sequences\n \n2. A FASTA alignment of (functionally related) homologous protein sequences AND\n a Phylogenetic Tree ensemble (trees in newick format)\n\nNAPA produces the following outputs:\n\n1. A mutation pair network (undirected for alignment only, directed/undirected for phylogeny ensemble)\n2. Network analysis - network communities, network node centralities, network path centralities\n\nDocumentation\n-------------\n\nPlease see the `documentation `_ on github for complete usage details.\n\nInstallation\n------------\n\nUse pip to install the napa package:\n\n.. code-block:: bash\n\n $ pip install napa\n\nNAPA depends on several other packages and these will be installed automatically by pip if they\nare not already installed. \n\n**Required packages:**\n\n* numpy\n* scipy\n* joblib\n* networkx\n* ete2\n* pyyaml\n\nNote the pip scipy installation can sometimes have issues. If so, alternate methods of installing scipy may be preferable. See scipy `install `_ for details. 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