BLAST+ Command Line Applications

The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
local similarity between sequences. The program compares nucleotide or
protein sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.

The Basic Local Alignment Search Tool (BLAST) is the most widely used
sequence similarity tool. There are versions of BLAST that compare
protein queries to protein databases, nucleotide queries to nucleotide
databases, as well as versions that translate nucleotide queries or
databases in all six frames and compare to protein databases or queries.
PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
with a protein query, and then uses that PSSM to perform further
searches. It is also possible to compare a protein or nucleotide query
to a database of PSSM’s. The NCBI supports a BLAST web page (at
blast.ncbi.nlm.nih.gov) as well as a network service. The NCBI also
distributes stand-alone BLAST applications for users who wish to run
BLAST on their own machines or with their own 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 (ncbi-blast).

Some useful links:

Help https://www.ncbi.nlm.nih.gov/books/NBK1762/
Manual https://www.ncbi.nlm.nih.gov/books/NBK279690/
Downloads ftp://ftp.ncbi.nih.gov/blast/executables/blast+/
Databases ftp://ftp.ncbi.nlm.nih.gov/blast/db/
ChangeLog http://www.ncbi.nlm.nih.gov/books/NBK131777
Reference https://www.ncbi.nlm.nih.gov/pubmed/20003500

Citing:
BLAST+: architecture and applications. Camacho C, Coulouris G, Avagyan
V, Ma N, Papadopoulos J, Bealer K, Madden TL. BMC Bioinformatics. 2009
Dec 15;10:421. doi: 10.1186/1471-2105-10-421.
