The JABAWS AACon service implements 17 different conservation scores for protein sequence alignments.

The majority of these scores were described by Valdar in 2002 (Scoring residue conservation. Proteins: Structure, Function, and Genetics 43(2): 227-241. PubMed or available on the Valdar Group publications page), but the SMERFs score was developed later and described by Manning et al. in 2008 (BMC Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51).

Enabling and disabling AACon calculations
When the AACon Calculation entry in the Web Services→Conservation is ticked, AACon calculations will be performed every time the alignment is modified. Selecting the menu item will enable or disable automatic recalculation.

Configuring which AACon calculations are performed
The Web Services→Conservation→Change AACon Settings ... menu entry will open a web services parameter dialog for the currently configured AACon server. Standard presets are provided for quick and more expensive conservation calculations, and parameters are also provided to change the way that SMERFS calculations are performed.
AACon settings for an alignment are saved in Jalview projects along with the latest calculation results.

Changing the server used for AACon calculations
If you are working with alignments too large to analyse with the public JABAWS server, then you will most likely have already configured additional JABAWS servers. By default, Jalview will chose the first AACon service available from the list of JABAWS servers available. If available, you can switch to use another AACon service by selecting it from the Web Services→Conservation→Switch Server submenu.