Unlike greedy algorithms (CD-HIT) or k-mer-based heuristics (MMseqs2), BlastClust performs a more thorough pairwise comparison, which can be more accurate for smaller, highly diverse sequence sets.

Since BlastClust is no longer included in the latest NCBI BLAST+ executables, you must download it as part of the package.

For Linux or macOS, use the tar command in your terminal: tar -zxvf blast-2.2.26-x64-linux.tar.gz Use code with caution.

You can strictly define the length coverage ( -L ) and sequence identity ( -S ) required to form a cluster.

If you are working with large-scale genomic data (millions of sequences), BlastClust may be too slow. NCBI and the broader community recommend these modern alternatives: Fast redundancy reduction CD-HIT Official Site MMseqs2 Massive datasets & sensitivity Ultra-High MMseqs2 GitHub BLAST+ Standard search & alignment NCBI BLAST+ Download 5. Troubleshooting Installation

Navigate to the NCBI FTP legacy directory to find the final stable releases of the classic BLAST toolkit.

is a legacy command-line utility developed by the National Center for Biotechnology Information (NCBI) for clustering protein or nucleotide sequences based on pairwise similarity. While it has been officially deprecated in favour of the modern BLAST+ suite, it remains a valuable tool for researchers who require high-accuracy, exhaustive all-to-all sequence alignments for smaller datasets. 1. How to Download BlastClust