v0.9.0-beta

🚀 Pre-release: SequenceAligner v0.9.0 (Beta)

Tag: v0.9.0-beta
Status: Pre-release (Testing & downstream modules pending)
Author: Abhinav Mishra

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✨ Features Implemented

• ✅ Three core alignment algorithms:
  • LCS (Longest Common Subsequence)
  • Global Alignment (Needleman–Wunsch)
  • Local Alignment (Smith–Waterman)
• ✅ FASTA input support with header-stripping
• ✅ Color-coded alignment output with position-aware formatting
• ✅ Modular and versioned implementation (main_v1.cpp, main_v2.cpp, main_v3.cpp)
• ✅ CMake-based build system with support for C++17
• ✅ MkDocs documentation and Doxygen API reference hosted via GitHub Pages
• ✅ Command-line usability with clear usage instructions

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⚠️ Known Limitations / To Be Done

• ❌ Testing coverage and validation for main_v2.cpp and main_v3.cpp is not yet complete
• ❌ No built-in scoring matrix customization (e.g., BLOSUM/PAM)
• ❌ Downstream analysis modules (e.g., result parsing, statistical summaries) are not yet implemented
• ❌ No graphical output or export of visualizations yet

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📦 Installation

git clone https://github.com/bibymaths/SequenceAligner.git
cd SequenceAligner
mkdir build && cd build
cmake ..
make

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🧪 Quick Usage

./aligner_v1 files/seq1.fasta files/seq2.fasta 2

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📚 Documentation

• Main docs: https://bibymaths.github.io/SequenceAligner/
• API docs: https://bibymaths.github.io/SequenceAligner/api/index.html

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📄 License

BSD 3-Clause License © 2025 Abhinav Mishra

What's Changed

• Added docs, make config, and api references by @bibymaths in #1

New Contributors

• @bibymaths made their first contribution in #1

Full Changelog: https://github.com/bibymaths/SequenceAligner/commits/v0.9.0-beta