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.