AACon is a set of tools implementing 17 different conservation scores reviewed by Valdar as well as the more complex SMERFS algorithm for predicting protein functional sites. AACon has been written with efficiency in mind and takes less than a second to calculate conservation by all 18 methods for an alignment of 500 sequences 350 residues long on a single CPU. AACon exploits parallelism for the more demanding methods and to allow multiple methods to run simultaneously. The parallel code gives close to linear speedup with the number of processors, thus making it suitable for server applications or other demanding environments.