Download BLAST Software and Databases
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications. For details, please see the BLAST+ user manual and the article in BMC Bioinformatics (PubMed link).
Installers and source code are available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ .
We strongly encourage users of the legacy C toolkit applications (e.g, blastall, blastpgp, etc.) to use the new BLAST+ applications. The BLAST+ applications have a number of new features and enhancements such as database masking, more flexibility in tabular formatting, indexed megaBLAST, and the ability to save results and reformat searches. Many of these are described in http://www.ncbi.nlm.nih.gov/pubmed/20003500
and http://www.ncbi.nlm.nih.gov/pubmed/18567917. More importantly, the BLAST+ applications use a completely redesigned framework that fixes a number of issues in the legacy applications:
1.) Extreme slowdown or failure to run with large queries. This is addressed by "query splitting" in the BLAST+ applications, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803857/figure/F2/
2.) Extreme slowdown or failure to run with large database sequences. This is addressed by "partial retrieval" in the BLAST+ applications, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803857/figure/F3/
3.) Inability to work with more than 65536 sequences at once (with an error message of "ObjMgrNextAvailEntityID failed with idx 2048"). This is a shortcoming of the older infrastructure and is not a problem with the BLAST+ applications.
A manual at http://www.ncbi.nlm.nih.gov/books/NBK1762/ describes how to set up and run the BLAST+ applications.
No new features will be added to the legacy applications, but periodic bugfix releases will be available in the interim from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/.
BLAST databases are updated daily and may be downloaded via FTP from ftp://ftp.ncbi.nlm.nih.gov/blast/db/. Database sets may be retrieved automatically with update_blastdb.pl, which is part of the BLAST+ suite. Please refer to the BLAST database documentation for more details.