16S_rRNA_phylogeny

Generate phylogenic tree form 16S ribosomal RNA

Install

Dependencies

Conda (skip if you already have conda installed)

Conda can be installed using these instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

Environment

Create a conda environment and install packages

conda create -n 16S -c conda-forge biopython=1.81 matplotlib=3.3.4 -y
conda activate 16S

PIP (Alternative to conda)

Altetrnatively, you can use pip:

pip install biopython==1.81 
pip install matplotlib

Muscle

mkdir apps
wget https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar xvfz muscle3.8.31_i86linux64.tar.gz -C apps
mv apps/muscle3.8.31_i86linux64 apps/muscle
chmod +x apps/muscle
rm muscle3.8.31_i86linux64.tar.gz

PhyML

wget http://www.atgc-montpellier.fr/download/binaries/phyml/PhyML-3.1.zip
unzip PhyML-3.1.zip -d apps
mv apps/PhyML-3.1/PhyML-3.1_linux64 apps/phyml
rm PhyML-3.1.zip

This Repo

wget https://github.com/TahaAslani/16S_rRNA_phylogeny/archive/refs/heads/main.zip
unzip main.zip
cp 16S_rRNA_phylogeny-main/* .
rm -r 16S_rRNA_phylogeny-main
rm main.zip

Data

Download 16S rRNA data from the following link: https://github.com/yphsieh/16S-ITGDB/tree/master/data

We need Sequence-based ITGDB: seq_itgdb_seq.fasta (sequence file) and seq_itgdb_taxa.txt (taxonomy file)

Run

Run command

bash Run.sh seq_itgdb_seq.fasta input_file output_folder

The input_file is a comma-separated text file. Each row is an organism and has two columns: The first column is the name of the organism (that you choose) and the second column is the corresponding code in the seq_itgdb_taxa.txt. Run the pipeline for the test_species.csv species

bash Run.sh seq_itgdb_seq.fasta test_species.csv Results

For other choice of species, look up their code in seq_itgdb_taxa.txt and replace them in test_species.