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

Project 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 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.

Release History

Release History

This version
History Node

1.1

History Node

0.88

History Node

0.86

History Node

0.85

Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
napa-1.1.tar.gz (39.6 kB) Copy SHA256 Checksum SHA256 Source Jan 17, 2017

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