CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+, compatibility with any BLAST+ version, real-time information regarding calculation progress and remaining run time, access to partial alignment results, queueing, pausing, and resuming BLAST+ calculations without information loss.