BioAlign v1.1.1:

Fixes

• Now using relative paths instead of full ones, hopefully fixing some problems with OneDrive.

BioAlign v1.1.0: Overhauled Pattern Matching and HTML Output

What's New in BioAlign 1.1.0?

BioAlign is a user-friendly tool for DNA sequence alignment and visualization that uses Clustal Omega for alignment and creates nicely formatted output documents with sequence highlighting.

New Features

• HTML Output Support: In addition to Word documents, BioAlign now generates HTML files for lightweight, browser-viewable results
• Improved Marking Algorithm: Completely overhauled pattern detection for more accurate results (some pattern were not detected in the old version)
• Cross-Line Pattern Matching: Now detects patterns that span across multiple lines of the same sequence correctly
• Enhanced Space-Ignoring Mode: Better support for finding patterns that cross triplet notation spaces
• Bug Fixes: Corrected issues with spaced marking functionality

Key Features

• Automatic DNA sequence alignment using Clustal Omega
• Triplet notation formatting for better readability
• DNA sequence search with customizable highlighting
• Support for both exact and space-ignoring search modes
• Output in both HTML and Word files
• Caching of alignment results for unchanged sequences

Usage

This release includes a Windows-ready package with the embedded Python runtime, Clustal Omega executable, and all required dependencies - ready to use without installation!

Simply:

1. Extract the 7z file to any location
2. Edit sequences.json with your DNA sequences
3. Run start.bat to launch the application
4. Follow the prompts to search and highlight sequence patterns

Output Files

• sequences.html: Open in any web browser for quick viewing
• sequences.docx: Word document with formatted alignment and highlighted matches

Notes

• This release is optimized for Windows systems
• Source code is available for developers to adapt for other platforms
• See the README.md file for full documentation
• Thank you for using BioAlign! I hope it simplifies your DNA sequence analysis tasks.

BioAlign v1.0.0: The first somewhat reliable and user-friendly release of BioAlign

What is BioAlign?

BioAlign is a user-friendly tool for DNA sequence alignment and visualization that uses Clustal Omega for alignment and creates nicely formatted Word documents with customizable sequence highlighting.

Key Features

• Automatic DNA sequence alignment using Clustal Omega
• Triplet notation formatting for better readability
• Powerful DNA sequence search with customizable highlighting
• Support for both exact and spaced search modes
• Color-coding options for different sequences
• Intelligent caching of alignment results for unchanged sequences

Usage

This release includes a Windows-ready package with the embedded Python runtime, Clustal Omega executable, and all required dependencies - ready to use without installation!

Simply:

1. Extract the 7z file to any location
2. Edit sequences.json with your DNA sequences
3. Run start.bat to launch the application
4. Follow the prompts to search and highlight sequence patterns

Notes

• This release is optimized for Windows systems
• Source code is available for developers to adapt for other platforms
• See the README.md file for full documentation
• Thank you for using BioAlign! I hope it simplifies your DNA sequence analysis tasks.