HTTPS SSH

ALVIS - Explorative Analysis and Visualisation of Multiple Sequence Alignments

Installation:

  • Download the ALVIS repository using "git clone https://bitbucket.org/rfs/alvis.git" 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 <<

Requirements:

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

Troubleshooting:

  • 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.

Documentation

License:

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 http://www.gnu.org/licenses/

Please cite:

Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw022 (http://nar.oxfordjournals.org/content/early/2016/01/26/nar.gkw022.full)
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

and:

BMC Proc. (2014) (http://bmcproc.biomedcentral.com/articles/10.1186/1753-6561-8-S2-S8)
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] cam.ac.uk

March 2016, Roland Schwarz