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pG-lt: An automated pipeline for phylogeney generation.

Project Description

pG-lt (or phyloGenerator-light) is a pipeline for the automated generation of phylogenies through Mass Phylogeny Estimation. It is adapted from phyloGenerator (C) 2013 and was written by D.J. Bennett with additional help and suggestions from W.D. Pearse, L. Hudson and A. Purvis.

It makes use of external programs for phylogeny generation and bioinformatics, these are: RAxML (Copyright (C) Stamatakis 2013), MAFFT (Copyright (C) 2013 Kazutaka Katoh) NCBI’s standalone BLAST suite 2.2.29+ and online API services (Copyright NCBI (C) 2009). It also uses the following python packages: Biopython (Copyright Cook (C) 2009), Dendropy (Copyright Sukumaran and Holder (C) 2010) and Taxon Names Resovler (Copyright (C) Bennett 2014).

For details on how to use pG-lt, please refer to its wiki: https://github.com/DomBennett/pG-lt/wiki For any questions or comments, feel free to email: dominic.john.bennett@gmail.com.

Copyright (C) 2015 Dominic John Bennett

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Release History

Release History

This version
History Node

v0.1-beta

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