A new version (2.5.0) of the BLAST+ executables is now available.
The new version offers support for HTTPS, accession.version as the primary sequence identifier, support for composition-based statistics with RPSTBLASTN, and a new taxonomic organism report. The release notes are at https://www.ncbi.nlm.nih.gov/books/NBK131777/
Two BLAST+ features require communication with the NCBI website (and HTTPS). First, the –remote flag sends the search to the NCBI for processing. Second, BLAST can take a sequence ID as a query and retrieve the sequence from the NCBI. You should update your BLAST+ executables by November 9, 2016 to ensure that these features continue to work. More information about the HTTPS transition is available at https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml
Improved support for accession.version as the primary identifier affects a number of BLAST+ executables. Blastdbcmd now produces FASTA from BLAST databases that has accession.version as the identifier rather than the traditional bar-delimited FASTA ID. See https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers for more information. Makeblastdb can now guess the type of ID (e.g., GenBank or Refseq) from the accession alone if the –parse_seqids flag is used. The search executables now produces reports identifying matches using accession.version by default.
The new executables are available on the NCBI FTP site at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST