Is Blastall Only Using Blast, Not Blast+?

Question

[Ken]

Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.

Answer 1

[Neilfws]

If your command line begins with "blastall", then you're running the older (not +) BLAST. Otherwise, if it begins with a BLAST program command such as blastn, then it's BLAST+.

Try some documentation.

[Michael Kuhn]

in doubt, believe the NCBI manual and not some third-party website that may or may not understand the difference between BLAST and BLAST+

[Ken]

Thanks neilfws, from ur reply, blastall is only use BLAST. However this web site implies when running blastall -p blastx, it is running the blastx+, isn't it? I quote from the site: "The first step is to download and install the BLAST+ tools onto your machine. Once you have done that you’ll find there are a number of different tools in the package. The main one that you will use to perform different blasts is blastall."

[Ken]

ok.. thanks neilfws and Michael.

Answer 2

[Semenko]

Any command starting with blastall is the old version of BLAST.

The NCBI "strongly encourage[s]" you to stop using the old blast tools (like blastall) and to download the BLAST+ rewrite:

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 ...

You can convert old BLAST scripts using blastall to the new BLAST+ syntax with the NCBI tool:

legacy_blast.pl [YOUR COMMAND] --print_only

If you really want to stick with blastall, the NCBI periodically fixes bugs in the old version, but won't improve it or add any new features: Old Blast FTP

[A.L]

The last link is dead. You can find versions of BLAST here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/