Important This software is no longer actively maintained, users are encouraged to migrate to SpreaD3.
Spatial Phylogenetic Reconstruction of Evolutionary Dynamics Version: 1.0.7, 2015 Authors: Filip Bielejec, Andrew Rambaut, Marc A. Suchard & Philippe Lemey Homepage: www.phylogeography.org License: LGPL
This is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This software 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 Lesser General Public License":http://www.gnu.org/licenses/lgpl.html for more details.
SPREAD is a Java program supporting processing and visualizations of BEAST's phylogeographic models ("BEAST software":http://beast.bio.ed.ac.uk/Main_Page).
Contains visualisations (templates), wrapped in a user friendly interface. Supported visualisations include embedded Processing applets and KML output for viewing in "Google Earth":http://www.google.com/earth or any other virtual globe software capable of reading the format.
A tutorial on using SPREAD is availiable "here":http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html
SPREAD: www.phylogeography.org/SPREAD PROCESSING libraries: http://processing.org/
Depends on the following libraries:
- jebl.jar
- core.jar
- colt.jar
- quaqua.jar (libquaqua64.jnilib, libquaqua.jnilib)
You're interested in contributing to SPREAD? THAT'S AWESOME! Here are the basic steps:
- fork SPREAD from here: http://github.com/phylogeography/SPREAD
- Hack, hack, hack!
- Document your changes in the Changelog
- Push the changes
- Send a pull request to the phylogeography/SPREAD project.
- Left panel stretches if a parsed attribute name is long
- (Continous Tree) Relate the HPD areas shown as polygons in GoogleEarth with specific nodes of the tree
- Rewrite Log file reader
- Mean tree calculation (from .trees file)
- Combobox for relaxed (from parser) / standard brownian motion (rate of 1)
- Annotate the terminals in the tree with corresponding taxon names
- Move all the parsing code to reader classes for trees -> avoid code duplication
- Add command line interface for kml templates
- Fix large scaling factor issues