MSA + Phylogeny Pipeline

A simple modular Bash pipeline to run multiple sequence alignment, trim it, and infer a phylogenetic tree using IQ-TREE 2.

🛠 Requirements

Option 1: ✅ Recommended: Conda

conda env create -f environment.yml
conda activate msa-phylo

This will install:

• MAFFT (multiple sequence alignment)
• TrimAl (automated trimming)
• IQ-TREE 2 (phylogenetic inference)

Option 2: ⚠️ Manual Install (not recommended)

sudo apt install mafft
sudo apt install trimal
conda install -c bioconda iqtree

📁 Structure

• input/sequences.fasta: your input sequences
• output/: all results will be saved here

▶️ Run the Pipeline

cd msa-phylo-pipeline/
chmod +x *.sh
./run_pipeline.sh

🔧 Configuration

You can change threads or memory by editing run_pipeline.sh:

THREADS=86
MEMORY=200G

🧪 Output Files

• output/aligned.fasta: MAFFT alignment
• output/aligned_trimmed.fasta: TrimAl-trimmed and reformatted alignment
• output/tree.treefile: Final phylogenetic tree from IQ-TREE

❗ Notes

• IQ-TREE will detect identical sequences and remove them by default (see .iqtree log).
• To retain duplicates, add --keep-ident to tree.sh.

📜 License

MIT