Enhance README.md by adding a comprehensive Table of Contents, Developer Setup instructions, and troubleshooting guidelines. This update improves documentation clarity and usability for both end users and developers.

Author: MasterGreenyMC

README.md

@@ -2,6 +2,26 @@
 
 BioAlign is a user-friendly tool for DNA sequence alignment and visualization. It uses Clustal Omega for alignment and creates nicely formatted Word documents with customizable sequence highlighting.
 
+## Table of Contents
+- [Features](#features)
+- [Installation](#installation)
+- [Usage](#usage)
+  - [Preparing Your Sequences](#preparing-your-sequences)
+  - [Running the Application](#running-the-application)
+  - [Search Options](#search-options)
+  - [Output](#output)
+- [Example](#example)
+- [Notes](#notes)
+- [Developer Setup](#developer-setup)
+  - [Installing Python Dependencies](#installing-python-dependencies)
+  - [Installing Clustal Omega](#installing-clustal-omega)
+  - [Required Files Structure](#required-files-structure)
+- [Requirements](#requirements)
+- [Troubleshooting](#troubleshooting)
+- [Contributing](#contributing)
+- [License](#license)
+- [Acknowledgements](#acknowledgements)
+
 ## Features
 
 - Automatic DNA sequence alignment using Clustal Omega
@@ -77,9 +97,87 @@ For the provided example sequences, searching for "CTG" with spaced mode enabled
 - The Word document uses Courier New font for consistent spacing
 - Highlighting uses yellow by default, or green/blue/pink when using separate colors
 
+## Developer Setup
+
+If you only want to work with the source code (main.py), you'll need to set up the following dependencies:
+
+### Installing Python Dependencies
+
+```bash
+pip install biopython python-docx
+```
+
+### Installing Clustal Omega
+
+1. **Windows**:
+   - Download Clustal Omega from http://www.clustal.org/omega/
+   - Extract the files to a directory named `clustal-omega-1.2.2-win64` in the same folder as main.py
+   - Ensure that `clustalo.exe` is directly inside this directory
+
+2. **macOS**:
+   - Install via Homebrew: `brew install clustal-omega`
+   - Modify the path in the prepare_seq function where Clustal Omega is called to use: `command_return = subprocess.run(f"clustalo --infile {input_file_name} --outfile {output_file_name} --outfmt clustal --force", shell=True)`
+
+3. **Linux**:
+   - Install via package manager: `sudo apt install clustal-omega` (Ubuntu/Debian) or equivalent
+   - Modify the path in the prepare_seq function where Clustal Omega is called to use: `command_return = subprocess.run(f"clustalo --infile {input_file_name} --outfile {output_file_name} --outfmt clustal --force", shell=True)`
+
+### Required Files Structure
+
+Create the following files in your working directory:
+- `main.py` - The main program
+- `sequences.json` - Your DNA sequences in JSON format
+- `start.bat` (optional) - For easy launching on Windows
+
 ## Requirements
 
-This package is self-contained and works on Windows systems without additional installations.
+For end users, the release package is self-contained and works on Windows systems without additional installations.
+
+For developers working with just the source code:
+- Python 3.6 or higher
+- Biopython library
+- python-docx library
+- Clustal Omega (installed as described above)
+- Access to write files in the working directory
+
+## Troubleshooting
+
+### Common Issues
+
+1. **"No module named 'Bio'"**
+   - Make sure you've installed Biopython: `pip install biopython`
+
+2. **"No module named 'docx'"**
+   - Make sure you've installed python-docx: `pip install python-docx`
+
+3. **"An error occurred while running clustal-omega"**
+   - Verify that Clustal Omega is installed correctly in the expected location
+   - Check that you have executable permissions for the Clustal Omega binary
+   - Try running Clustal Omega manually to verify it works outside the application
+
+4. **"ModuleNotFoundError: No module named 'sequences'"**
+   - Ensure that `sequences.json` exists in the same directory as main.py
+   - Check that the JSON file is properly formatted
+
+5. **Word document has no highlighting**
+   - Make sure you entered a valid sequence pattern that exists in your DNA sequences
+   - Verify you selected the appropriate search mode for your pattern
+
+## Contributing
+
+Contributions to improve BioAlign are welcome! Here's how you can contribute:
+
+1. Fork the repository
+2. Create a feature branch: `git checkout -b new-feature`
+3. Make your changes
+4. Test your changes thoroughly
+5. Submit a pull request with a clear description of the improvements
+
+Please ensure your code maintains compatibility with the existing functionality and follows the project's coding style.
+
+## License
+
+This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.
 
 ## Acknowledgements