This release introduces command-line parameters for flexible usage, allowing users to specify:
--msa_file: Path to the input multiple sequence alignment file--clstr_file: Path to the CD-HIT cluster file--output_file: Path to save the resulting substitution matrix--nproc: Number of CPU cores to use for parallel computation
Additional improvements:
- Optimised performance for large datasets (>30k sequences)
- Henikoff weighting and BLOSUM-style log-odds scoring
- Updated documentation and examples for CLI usage