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h1. SPREAD
Spatial Phylogenetic Reconstruction of Evolutionary Dynamics
Version 1.0.2, 2011
Filip Bielejec, Andrew Rambaut, Marc A. Suchard & Philippe Lemey
h1. LICENSE
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.
h1. PURPOSE
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
h1. SUPPORT & LINKS
SPREAD: www.phylogeography.org/SPREAD
Processing libraries: http://processing.org/
Suggestions or bug reports:
<filip.bielejec(_sorry_spybots_)rega.kuleuven.be>
h1. COMPILING
Depends on the following libraries:
* jebl.jar
* org.boehn.kmlframework_20090320.jar
* core.jar
* colt.jar
* ColorPicker.jar
* quaqua.jar (libquaqua64.jnilib, libquaqua.jnilib)
Before exporting to a runnable jar change line 12 in templates.MapBackground.java:
boolean fromJar = false
to
boolean fromJar = true
h1. TODO
* get rid of impute argument from time slicer templates and GUI
* improve custom slice heights
* Add command line interface for kml templates
* Templates: collect data into ArrayList<Layer>, then pass it to KML Generator or Processing canvas. This way all the exceptions are caught beforehand.
* Fix large scaling factor issues
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