Command-line equivalent of online BLAST Needleman-Wunsch Global Alignment interface

Question

[James Denvir]

I was slightly surprised to find the online version of BLAST has an interface for global (Needleman-Wunsch) alignment.

Is there an equivalent command-line interface for this in the standalone version of BLAST? As far as I can tell from blastn -help, the command line version only runs local alignment.

[GenoMax]

Even though it is available under the general tool heading of blast NCBI may be using a standard N-W implementation for global alignments. You could email blast support ([e-mail]) and confirm.

If you need a command line equivalent to use now then Needle from EMBOSS should work.

[James Denvir]

Thanks for the comment. I was aware of Needle, but I've been using the command line version of blast and was just wondering if I could get away without another software dependency... The help for N-W on the online version I linked mentions the algorithm employs memory-use optimizations - which makes it sound like there may be some implementations that are non-standard in some sense. The link describing those is broken, which suggests this interface isn't in wide use, so probably Needle is the way to go.