ALVIS - Explorative Analysis and Visualisation of Multiple Sequence Alignments


  • Download the ALVIS repository using "git clone" or download the binary release from the downloads section.
  • In case of the latter, unzip the archive to a folder of your choice and execute the JAR using >> java -jar Alvis.jar <<


  • Java 7
  • OPTIONAL: R with a working rJava installation and the "kernlab" package installed for some advanced features


  • Should you encounter out-of-memory errors, start Alvis with the additional JVM command line switch -xMx4096 for 4GB of RAM (adjust to your system)
  • Getting rJava to work can prove difficult. Please consult the rJava documentation for support, most Alvis features are available without it.



Copyright 2015 - Roland Schwarz, Asif Tamuri, Science Practice

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License version 3 as published by the Free Software Foundation. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License version 3 for more details. You should have received a copy of the GNU Affero General Public License version 3 along with this program. If not, see

Please cite:

Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw022 (
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments
Roland F. Schwarz, Asif U. Tamuri, Marek Kultys, James King, James Godwin, Ana M. Florescu, Jörg Schultz and Nick Goldman


BMC Proc. (2014) (
Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs
Marek Kultys, Lydia Nicholas, Roland Schwarz, Nick Goldman and James King

For questions and bug reports, please contact me at

rfs32 [at]

March 2016, Roland Schwarz