Ion Flux contributed major performance improvements to the latest version (2011Sep11) of ANNOVAR.

From the ANNOVAR website:

2011Sep11: New Version of ANNOVAR is released with significant speedup of filter operation for certain databases (dbSNP, SIFT, PolyPhen, 1000G, etc). In previous version of ANNOVAR, filter-based annotation for ex1.human (12 variants) requires ~10 minutes for snp132, sift or polyphen. In the new version, it takes 1 second only! […]

We like to see open-source software projects thrive, and we’re happy to contribute where we’re able to do so. Thanks to ANNOVAR’s author, Kai Wang, for providing such a useful piece of software, and to Ion Flux engineer Marine Huang for optimizing the implementation.