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Welcome to the AACon 1.1 website

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.

AACon is available as a SOAP web service, a stand alone Java executable and a Java library with concise API for accessing all the conservation methods programmatically. The executable runs on all platforms that support Java version 6 and above (Windows, Unix/Linux, Mac).

Since December 2011, over 15,000 AACon calculations have been performed through the popular sequence analysis program Jalview and JABAWS servers.

Jalview: Sequence Alignment


AACon the standalone executable and the Java Library

The standalone executable is for calculating conservation from the command line. The Java library provides simple API for the Java developers who want to have AACon functionality from their applications. The executable and the library comes from the same jar file and will work on any operation system that supports Java.

  • Command line executable and the Java library: download

Help with a command line client is available from standalone executable page. The library is described on the library page.

Web service client

The AACon web service, is a standard SOAP web service and thus you can use your favorite programming language to access it. That's more, to simplify the use of web service even further, we offer a Java web service client. This client can submit the tasks to a web service, retrieve the results and thus can be used in place of the command line client. Alternatively, it can serve as an example of coding against AACon web service.

Please refer to web service help page for a help on using AACon web service.

Source code

AACon is an open source project. If you want to contribute or report an issue have a look at our GitHub repository.

If you want to extend AACon download the command line executable and the Java library source code. AACon source code is licensed under Apache 2 licence.

New in AACon 1.1

Some minor bugs have been fixed and the website and documentation were improved:

  • Conservation scores are now reported as three decimal place numbers, for both method outputs and normalisations.
  • Sphinx is now used to generate our documentation pages.
  • Documentation was updated to reflect the latest changes introduced in the project.


If you have any issues, questions or suggestions feel free to contact us on


Agnieszka Golicz, Peter V. Troshin, Fábio Madeira, David M. A. Martin, James B. Procter and Geoffrey J. (2018) AACon: A Fast Amino Acid Conservation Calculation Service Submmitted paper.


JABAWS and AACon are part of the "Dundee Resource for Protein Sequence analysis and structure prediction", which is an ELIXIR-UK resource.

Site Last updated: 22 January 2018 by Fábio Madeira. This site was built using the Bootstrap framework.