NCBI BLAST

This is a version of BLAST provided by NCBI. The default options are tuned for speed so it is important to learn about the options which can be tweaked to get optimal results to your questions. The BLAST book has an excellent treatment of the options. The tool lacks some of the advanced options supported by WU BLAST but recently improvements to the code base, speed improvements, have made this tool a good choice for most questions.

Details at http://www.ncbi.nlm.nih.gov/BLAST