Conservation

Conservation is a Python package for evolutionary conservation analysis at the codon and amino acid level. It supports comparative analysis using Pfam domain sequences and CDS datasets across multiple species.

🔧 Features

• Codon substitution matrix computation
• Fisher's exact test for conservation significance
• Automated visualization of alignment and substitution matrices
• Supports BLOSUM62 alignment, multi-threading, and multiple species

📦 Installation

You can install the package from PyPI:

pip install conservation

Or from Bioconda:

conda install bioconda::conservation

Or install from source:

git clone https://github.com/hanjunlee21/conservation.git
cd conservation
pip install .

🚀 Usage

conservation codon \
  --domain domain.fasta \
  --cds species1.fasta,species2.fasta \
  --output results_dir \
  --threads 4

Command-line Arguments

• --domain, -d: Pfam or domain FASTA file
• --cds, -c: Comma-separated list of CDS FASTA files (one per species)
• --output, -o: Output directory
• --threads, -t: Number of parallel threads
• --fdr, -q: FDR cutoff (optional)
• --conservedness, -s: Identity ratio threshold (optional)
• --dpi, -r: DPI for PDF plots

📊 Outputs

• Codon substitution matrix .tsv
• Statistical analysis .statistics.tsv
• PDF visualizations of alignments and substitution matrices

🧬 Example

Example command for 3 species:

conservation codon \
  -d pfam_domain.fasta \
  -c human.fasta,mouse.fasta,yeast.fasta \
  -o conservation_output

📁 Project Structure

conservation/
├── conservation/
├── ├── lib/
│   ├── └── N34_modifications.tsv
│   ├── __init__.py
│   ├── commands.py
│   ├── conservation_codon.py
│   └── version.py
├── bin/
│   └── conservation
├── README.md
├── setup.py
├── pyproject.toml
└── ...

📜 License

MIT License

👤 Author

Hanjun Lee
hanjun_lee@hms.harvard.edu

Project URL: https://github.com/hanjunlee21/conservation