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