<p align="center">
<img src="https://raw.githubusercontent.com/ivanmugu/homologyviz/refs/heads/main/src/homologyviz/images/logo.png" alt="HomologyViz" width="450">
</p>
<div align="center">
![PyPI Version](https://img.shields.io/pypi/v/homologyviz)
![GitHub License](https://img.shields.io/github/license/ivanmugu/homologyviz)
![Python](https://img.shields.io/badge/python-3.11-blue.svg)
</div>
---
# Make a graphical representation of BLASTn alignments
Homology Visualization (HomologyViz) uses GenBank files (.gb) to align the sequences and plot the genes. HomologyViz uses the information from the `CDS` features section to plot the genes. To customize the colors for plotting genes, you can add a `Color` tag in the `CDS` features with a color in hexadecimal. For example, add the tag `/Color="#00ff00"` to show a green gene. Or, you can edit the colors interactively in the plot.
HomologyViz is an easy-to-use option for people with little coding knowledge. The program uses Dash for an interactive and web-friendly experience. HomologyViz is a flexible app that allows you to export your graph in different formats and sizes for publication quality.
## Requirements
- [blastn](https://www.ncbi.nlm.nih.gov/books/NBK569861/) must be installed
locally and in the path
HomologyViz has been tested in Chrome using macOS.
## Installation
First, create a virtual environment with `conda` or `venv`. Then, install
homologyviz using pip as follows:
```bash
pip install homologyviz
```
## Usage
To run the app type:
```bash
homologyviz
```
Output:
<p align="center">
<img src="https://raw.githubusercontent.com/ivanmugu/homologyviz/refs/heads/main/src/homologyviz/images/HomologyViz_app.png" alt="HomologyViz" width="600">
</p>
## Credits
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. Also, if you have any suggestions, let me know, and I will try to implement them.
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