This is the first release candidate for FUNC-E v2.0. This version represents a complete write of FUNC-E using Python (previous version was Perl). The functionality is the same but with the follow changes: Some command-line options have changed. There is no longer a preset option. The output files are different and module directories are no longer created. Bugs were fixes in both the count of terms and the module clustering. FUNC-E now provides an API for use in Python scripts. New functions are available for automatic retrieval of GO, KEGG and InterPro terms so users don't have to collect these on their own.