|2. Loading Data||3. Running the Data Analysis algorithms||4. The PHYLOViZ Display Interface||5. Querying and Visualizing the data|
PHYLOViZ core and several plugins are free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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 General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
Certain source files distributed by the PHYLOViZ Team are under the terms of the GNU General Public License Version 3 with the following clarification and special exception, but only where PHYLOViZ Team has expressly included it in the particular source file's header.
Linking this library statically or dynamically with other modules is making a combined work based on this library. Thus, the terms and conditions of the GNU General Public License cover the whole combination. As a special exception, the copyright holders of this library give you permission to link this library with independent modules to produce an executable, regardless of the license terms of these independent modules, and to copy and distribute the resulting executable under terms of your choice, provided that you also meet, for each linked independent module, the terms and conditions of the license of that module. An independent module is a module which is not derived from or based on this library. If you modify this library, you may extend this exception to your version of the library, but you are not obligated to do so. If you do not wish to do so, delete this exception statement from your version.
Code licensed under this license may be reused in commercial products provided that changes made directly in the sources - bug fixes or enhancements - must be contributed back to PHYLOViZ, but new source files (as in new plugins) which you write that link to PHYLOViZ code do not need to be.
Choose the appropriate version for your operating system or the .jar file. The OS specific versions already contain some memory specific parameters to enhance the software performance when using large datasets.
See details about available plugins and the licenses under which they are covered.
Platform specific packages (click on the icon to download):
- Mac OS X (.tgz)
Just unzip the package and run either
bin/phyloviz accordingly to your operating system. Note that you must have a JRE environment installed. You may need to change some default parameters, such as memory requirements, in
NOTE: You may need to adjust some parameters in
with respect to memory usage. These settings have a strong impact on
visualization features. For instance, in Windows, you may achieve better results with:
default_options="--branding phyloviz -J-Xss8M -J-Xms32m -J-Xmx1024M --laf javax.swing.plaf.metal.MetalLookAndFeel"
IMPORTANTE NOTICE: After installing always go to the "Help" menu and "Check for updates" to install any novel plugins or latest updates to PHYLOViZ software. The SNP analysis plugin is installed in this way to demonstrate the plugin capability.
To access the previous beta version of Phyloviz please follow this link.
All the Source code is available in the new code repository for in bitbucket.org. Check it out inhttp://code.phyloviz.net/.
After downloading the latest version of PHYLOViZ, you can start the tutorial in the following link: Loading Data