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napa 1.1

Network Analysis of Protein Adaptation (intra-protein residue coevolution network construction and analysis)

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.

 
File Type Py Version Uploaded on Size
napa-1.1.tar.gz (md5) Source 2017-01-17 38KB