Metadata-Version: 1.1
Name: napa
Version: 1.2
Summary: Network Analysis of Protein Adaptation (intra-protein residue coevolution network construction and analysis)
Home-page: http://karchinlab.org/apps/appNapa.html
Author: Violeta Beleva Guthrie
Author-email: vbeleva@gmail.com
License: UNKNOWN
Description: NAPA - Network Analysis of Protein Adaptation
        ---------------------------------------------
        
        The NAPA package performs intra-protein residue coevolution network construction and analysis.
        
        The package supports two input types:    
        
        1. A FASTA alignment of (functionally related) homologous protein sequences
         
        2. A FASTA alignment of (functionally related) homologous protein sequences AND
           a Phylogenetic Tree ensemble (trees in newick format)
        
        NAPA produces the following outputs:
        
        1. A mutation pair network (undirected for alignment only, directed/undirected for phylogeny ensemble)
        2. Network analysis - network communities, network node centralities, network path centralities
        
        Documentation
        -------------
        
        Please see the `documentation <https://github.com/KarchinLab/NAPA/wiki>`_ on github for complete usage details.
        
        Installation
        ------------
        
        Use pip to install the napa package:
        
        .. code-block:: bash
        
            $ pip install napa
        
        NAPA depends on several other packages and these will be installed automatically by pip if they
        are not already installed.  
        
        **Required packages:**
        
        * numpy
        * scipy
        * joblib
        * networkx
        * ete2
        * pyyaml
        
        Note the pip scipy installation can sometimes have issues.  If so, alternate methods of installing scipy may be preferable.  See scipy `install <http://www.scipy.org/install.html>`_ for details.  Then rerun pip install napa.
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
