Phylogenetic and Molecular Evolution (PhaME) analysis tool

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.

Installing PhaME

PhaME can be installed and used in following ways:

1. Using conda directly

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 conda-forge
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels r

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

THen run phame:

phame phame.ctl

2. Using conda to separately install all dependencies and get the develop version from github:

Create a separate conda environment:

conda create -n phame_env

Install required dependencies into the environment

conda install -c bioconda perl-bioperl -n phame_env --yes
conda install -c bioconda samtools bcftools -n phame_env --yes
conda install -c bioconda mummer -n phame_env --yes
conda install -c bioconda bowtie2 -n phame_env --yes
conda install -c bioconda bwa -n phame_env --yes
conda install -c bioconda fasttree -n phame_env --yes
conda install -c bioconda bbmap -n phame_env --yes
conda install -c bioconda raxml -n phame_env --yes
conda install -c bioconda perl-parallel-forkmanager -n phame_env --yes
conda install -c bioconda iqtree -n phame_env --yes
conda install -c bioconda perl-statistics-distributions -n phame_env --yes
conda install -c bioconda paml -n phame_env --yes
conda install -c bioconda mafft -n phame_env --yes
conda install -c bioconda hyphy -n phame_env --yes

Clone the latest github repo:

git clone https://github.com/LANL-Bioinformatics/PhaME.git

Then test phame to see if the installation was complete using a short test run:

source activate phame_env
cd PhaME
test/TestAll.sh 1

CITATION

Shakya, M., Ahmed. S.A, Davenport K.W., Flynn M.C., Lo. C-C, Chain P.S.G. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Sci. Rep. 10, 1723 (2020).

doi: https://doi.org/10.1038/s41598-020-58356-1

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Contact

Migun Shakya Patrick Chain

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ACKNOWLEDGEMENTS

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.].

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Copyright

Copyright (2018). Triad National Security, LLC. All rights reserved.

This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration.

All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

This is open source software; you can redistribute it and/or modify it under the terms of the GPLv3 License. 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. Full text of the GPLv3 License can be found in the License file in the main development branch of the repository.