Interactive Genomics Dashboard

📊 Interactive Genomics Dashboard

Streamlit app to align FASTA sequences, compute k‑mer stats, find & highlight motifs, build identity matrices, infer phylogenies (FastTree / IQ-TREE), and auto‑generate a narrative for general‑audience or technical readers. State is preserved with st.session_state, so changing k‑mers, motifs, or story mode doesn’t recompute everything.

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🖼️ UI Preview

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🚀 Quick start

1. Clone

   git clone https://github.com/chalco777/dna_stats_app
   cd dna_stats_app

2. Create environment (conda/mamba) or use pip

   mamba env create -f environment.yml
   mamba activate genomics-dashboard

3. (Recommended) Install external binaries

   conda install -c bioconda mafft clustalo fasttree iqtree

4. Run

   streamlit run app_en.py

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✨ Features

• FASTA upload & header cleanup
• Multiple sequence alignment (MAFFT / Clustal Omega)
• Identity matrix (styled) + CSV export
• Motif search & highlighting
• Conservation profile (gap‑penalized or not)
• Phylogenetic tree (FastTree or IQ-TREE) with interactive viewer (PhylocanvasGL)
• Auto “story” in General‑audience or Technical tone
• Persistent UI state with st.session_state

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📂 Project structure

├── app_en.py # English version
├── app_es.py # Spanish version
├── requirements.tx
├── environment.yml
├── data/ # optional example FASTA files
├── docs/ # screenshots

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🧪 Example data

Put small demo FASTA files under data/ and upload them via the UI.
(If you add CLI flags to auto-load examples, document them here.)

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⚙️ Requirements

Python ≥ 3.10

Python libs (see requirements.txt / environment.yml): streamlit, numpy, pandas, matplotlib, etc.

External tools (optional but needed for full functionality):

• MAFFT
• Clustal Omega
• FastTree
• IQ-TREE 2

Ensure binaries are on your $PATH.

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🧠 How it works (high level)

1. Parse FASTA, normalize headers.
2. Align sequences (MAFFT or Clustal Omega).
3. Compute identity matrix & conservation profiles.
4. Infer tree (FastTree or IQ-TREE) in a temp dir; render with PhylocanvasGL.
5. Generate a narrative summary (general vs technical).

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📸 More screenshots

Statistics tab

Identity matrix

Motif search

Multiple sequence alignment

Conservation profile

Tree viewer

Story tab

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❗ Troubleshooting

IQ-TREE exit status 2
→ Use --redo or a unique --prefix each run.

“No tree file produced”
→ Check that the model string is valid (e.g., GTR+G), and outputs are written inside the temp dir.

Alignment empty / crashes
→ Verify FASTA formatting and headers. Ensure ≥2 sequences.

Thread warnings
→ Use -T AUTO for IQ-TREE on small alignments.

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📚 Cite the tools

If you publish results produced with this app, please cite (add full references):

• Katoh & Standley (2013) – MAFFT
• Sievers et al. (2011) – Clustal Omega
• Price et al. (2010) – FastTree
• Minh et al. (2020) – IQ-TREE 2
• PhylocanvasGL project
• Streamlit

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🤝 Contributing

Issues and PRs are welcome.
Open an issue first for major changes; add screenshots/tests when relevant.

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📬 Contact

Julio Orellana-Montes
julio.orellana@upch.pe

Adrian Chalco-Gonzalez
adrian.chalco@upch.pe