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Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
PhaME can be installed using conda. If you do not have anaconda or miniconda installed, please do so. Installation of miniconda or anaconda is rather straight forward. See here. After installtion of conda, add channels for bioconda and conda-forge using:
$ conda config --add channels r
$ conda config --add channels defaults
$ conda config --add channels conda-forge
$ conda config --add channels bioconda
Then simply run:
conda install phame
We do recommend creating a separate conda environment for PhaME. You can create a conda environment by:
$ conda create -n my_env
$ conda install phame -n my_env
To get the latest version of PhaME, one can use "git" to obtain the package:
$ git clone https://github.com/mshakya/PhaME.git
$ cd PhaME
$ ./INSTALL.sh
However, ./INSTALL.sh is no longer supported. We recommend using bioconda to install all dependencies of PhaME and the git clone the repository to use the latest PhaME.
From raw reads to trees: Whole genome SNP phylogenetics across the tree of life.
Sanaa Afroz Ahmed, Chien-Chi Lo, Po-E Li, Karen W Davenport, Patrick S.G. Chain
bioRxiv doi: http://dx.doi.org/10.1101/032250
This project is funded by U.S. Defense Threat Reduction Agency [R-00059-12-0 and R-00332-13-0 to P.S.G.C.].
Copyright (c) 2018, Los Alamos National Security, LLC All rights reserved.
Copyright 2018. Los Alamos National Security, LLC. This material was produced under U.S. Government contract DE-AC52-06NA25396 for Los Alamos National Laboratory (LANL), which is operated by Los Alamos National Security, LLC for the U.S. Department of Energy. The U.S. Government has rights to use, reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR LOS ALAMOS NATIONAL SECURITY, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from LANL.
Additionally, 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. Accordingly, 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.