🧬 Create visual representations of BLASTn alignments

HomologyViz is a Python-based web app for visualizing pairwise BLASTn alignments between DNA sequences with gene annotations and customizable color maps. It allows you to explore homologous regions and gene structures interactively, with publication-ready output.

HomologyViz reads GenBank files (.gb), uses the CDS features to plot genes as arrows, and performs local BLASTn alignments between sequences. Homology regions are colored by identity percentage using a flexible, user-selectable color scale.

You may optionally customize gene colors directly in the GenBank file by adding a /Color tag to a CDS feature. For example, /Color="#00ff00" will render that gene in green. You can also edit gene colors interactively using the web interface.

HomologyViz is ideal for researchers and students with little or no coding experience. It runs locally and requires no cloud deployment or server hosting.

🚀 Features

• Interactive plots of aligned DNA sequences
• Gene annotations rendered as directional arrows
• Homology regions colored by % identity using customizable color scales
• Click-to-select genes or regions and change their color
• Exportable visualizations (SVG, PNG, PDF, HTML)
• Built with Dash and Plotly

🖼 Example

✅ Requirements

• Python 3.11, 3.12
• blastn (part of BLAST+) must be installed and available in your system PATH if installing via pip or git clone.

HomologyViz has been tested in Google Chrome on macOS, but should work across all modern browsers and platforms.

📦 Installation

• Using pip:

python3.12 -m pip install homologyviz

• Cloning this repository:

git clone https://github.com/yourusername/homologyviz.git
cd homologyviz
python3.12 pip install .

• Using conda:

conda create -n homologyviz python=3.12 pip
conda activate homologyviz
pip install homologyviz

🧪 Usage

Once installed, launch the app by typing:

homologyviz

📚 Documentation

You can find the full documentation for HomologyViz at:

👉 https://homologyviz.readthedocs.io

👤 Author

Created by Iván Muñoz Gutiérrez, PhD
Montana State University
Department of Microbiology & Cell Biology
Github: @ivanmugu

🙏 Acknowledgments

• Built on Dash, Plotly, and Biopython
• Inspired by easyfig: Sullivan et al (2011) Bioinformatics 27(7):1009-1010

📄 License

BSD 3-Clause License

📝 Notes

• I am developing HomologyViz in my free time, so if you find a bug, it may take me some time to fix it. However, I will fix the problems as soon as possible.
• If you have any suggestions, let me know, and I will try to implement them.