BLAST+ 2.2.15 is now available. The new release can run multithreaded searches faster and can focus your searches by organism groups more easily.

Automatic threading model switching
BLAST+ can now run 2-10x faster for small databases and large numbers of queries when you use multiple threads (CPUs). BLAST will now automatically select the fastest threading model (ThreadByQuery or ThreadByDatabase) for your search.

Details

New taxonomy limit option
You can now also limit your search to sequences from a group of organisms without first using a custom script to get all species-level Taxonomy IDs (taxids) for the group.

Details

You can use the NCBI Taxonomy Browser to find taxids

Combining options
These two new features can work together to deliver more targeted and faster search results. When limiting your search by organism, you search a smaller database and BLAST can automatically switch to the faster search mode. Plus, the organism limit means you only see relevant matches.

Example
The command-line below combines multithreading (-num_threads 16) and an organism limit that restricts the search to sequences from bacterial genus Helicobacter (-taxid 209). See the BLAST® Command Line Applications User Manual for more information on command-line options.

blastn -db nt -query sampleQueryFile.fa -num_threads 16 \
-taxids 209 -out H_pylori.out