Are there some faster alternatives to BLAST (specifically nucleotide BLAST)? I like that I can search through all GenBank+EMBL+DDBJ+PDB+RefSeq sequences (nt collection), but I feel like there must be a faster way. If I wanted to identify thousands or millions of sequences, it's somewhat inefficient.
I guess what I was really asking for is a metagenomic classifier. There are a few of those out there:

 - Kraken: https://ccb.jhu.edu/software/kraken/
 - GOTTCHA: http://lanl-bioinformatics.github.io/GOTTCHA/
 - CLARK: http://clark.cs.ucr.edu/
 - MetaPhlAn: http://huttenhower.sph.harvard.edu/metaphlan

Sure, these are not exactly same as BLAST, but if you need to quickly classify a lot of reads, these tools will do that.