ETE-NPR is a bioinformatics program providing a complete environment for the execution of phylogenomic workflows, including super-matrix and family-tree reconstruction approaches. ETE-NPR covers all necessary steps for high quality phylogenetic reconstruction, from alignment reconstruction and model testing to the generation of publication ready images of the produced trees and alignments. ETE-NPR is built on top of a bunch of specialized software and comes with a number of predefined workflows.

If you use ETE-NPR in a published work, please cite:

   Jaime Huerta-Cepas, Peer Bork and Toni Gabaldon. In preparation. 

(Note that a list of the external programs used to complete the necessary computations will be also shown together with your results. They should also be cited.)

Homepage:   http://etetoolkit.org/ete_npr/ 
Contact:    huerta [at] embl.de & tgabaldon [at] crg.es

This document describes how to install ETE-NPR from sources in a Linux environment. Note that the recomended approach for most of the users is to use the portable or virtual package available at http://etetoolkit.org/ete_npr.

However, building ETE-NPR from sources will provide a better performance than the portable packages.

https://github.com/jhcepas/npr/releases

  python
  python-numpy
  python-qt4 (optional, required for image generation)

You will need also basic tools for compiling (gcc, g++). As an examples, the 'build-essential' package (in ubuntu) should be enough. You may also need to install 'automake' and 'autoconf'

Some of the external programs require special libs that might not be installed. Most commonly:

   libargparse-dev

You need to clone the following repository* at the root* of the npr/ directory:

   $ cd npr/
   $ git clone http://github.com/jhcepas/ext_apps.git 

Enter the ext_app directory and run the compile script

   $ cd npr/ext_apps/
   $ bash compile.sh all

   $ cd npr/
   $ ./npr check