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# 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 ## * A preliminary user guide is available inside the "doc" folder. * A demonstration / tutorial video can be found here: https://www.youtube.com/watch?v=fWyRoxv-DBM ## 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/ ## Useful Links: ## * Try the web version of the software at: http://science-practice.com/projects/sequence-bundles/ ## 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