Copyright 2016 by Shawn Rupp
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 3 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.
Python 3
Python 3 version of Biopython
PAML (if using CodeML)
PhyML (if using CodeML for multiple species alignments)
AlignmentProcessor is a pipeline meant to quickly convert a multi-fasta alignment file into a format that can be read by KaKs_Calculator or PAML and optionally run those programs. When running CodeML, alignment processor will use an input control file as a template to create a unique control for each gene. It will call PhyML to create a unique phylogenic tree for each gene based off of its sequences.
You can run the AlignmentProcessor wrapper which will call all of the python scripts in sequence, or you may call each script individually.
AlignmentProcessor is freely available on GitHub and can either be downloaded directly from the site, can cloned using the following command:
git clone https://github.com/WilsonSayresLab/AlignmentProcessor.git
Since Biopython offers the fastest and easiest ways to deal with alignments in a python script, it is used in several of the scripts in this package. The easiest way to install Biopython is to download a Python 3 version Anaconda (https://www.continuum.io/downloads). AlignmentProcessor was written in Python 3, but Python 3 will be installed alongside Anaconda, so you don't need to worry about that if you use Python 2.
Once Anaconda is installed, all you have to do is paste the following into a terminal and Anaconda will install Biopython for you:
conda install -c https://conda.anaconda.org/anaconda biopython
AlignmentProcessor0.21 is packaged with KaKs_Calculator2.0 binaries for Linux and Windows, and a KaKs_Calculator1.2 binary for Mac (there is no 2.0 binary available for OSX). Before using, copy or move the appropriate binary for your system into the AlignmentProcessor bin which contains the python scripts.
If you plan to use CodeML, you must first download PAML (http://abacus.gene.ucl.ac.uk/software/paml.html) and move the folder into the AlignmentProcessor directory. Make sure that it is titled "paml".
If you plan to use CodeML, you must also download PhyML (http://www.atgc-montpellier.fr/phyml/binaries.php). Similar to PAML, you must move the folder into the AlignmentProcessor directory and change the name of both the folder and the binary for your operating system to "PhyML".
python AlignmentProcessor.py --axt/phylip --kaks/codeml -r <reference species> -i <input fasta file> -o <path to output directory>