nguyenngochuy91/Gibberellin-Operon

Gibberellin-Operon

Purpose

ROAGUE is a tool to reconstruct ancestors of gene blocks in prokaryotic genomes. This repo is an application of ROAGUE on operon Gibberellin.

Requirements

• Wget
• Conda (package manager so we don't have to use sudo)
• Python 3+
• Biopython 1.63+
• Clustalw
• Muscle Alignment
• BLAST+
• ETE3 (python framework for tree)
• PDA (optional if you want to debias your tree base on Phylogenetic Diversity)
• Prokka (bacterial genome annotation tool)

Installation

Users can either use github interface Download button or type the following command in command line:

git clone https://github.com/nguyenngochuy91/Ancestral-Blocks-Reconstruction

Install Miniconda (you can either export the path everytime you use ROAGUE, or add it to the .bashrc file). Before using the following command line, users will need to install Wget.

wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda_ete/
export PATH=~/anaconda_ete/bin:$PATH;

Install Biopython and ete3 using conda (highly recommended install biopython with conda)

conda install -c bioconda biopython ete3

Install ete_toolchain for visualization

conda install -c etetoolkit ete_toolchain

Install BLAST, ClustalW, MUSCLE, Prokka

conda install -c bioconda blast clustalw muscle prokka

For PDA, check installation instructions on this website: PDA

Usage

The easiest way to run the project is to execute the script ROAGUE, the results are stored in directory ancestral_reconstruction, under the name Ryan_operon, Ryan_rpoB,Ryan_operon_64,Ryan_rpoB_64

./ROAGUE.py