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README.rst

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 on github for complete usage details.

Installation

Use pip to install the napa package:

$ 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 for details. Then rerun pip install napa.

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