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SPREAD

Spatial Phylogenetic Reconstruction of Evolutionary Dynamics
Version 1.0.1, 2011
Filip Bielejec, Andrew Rambaut, Marc A. Suchard & Philippe Lemey

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 for more details.

PURPOSE

SPREAD is a Java program supporting processing and visualizations of BEAST’s phylogeographic models (BEAST software).

Contains visualisations (templates), wrapped in a user friendly interface. Supported visualisations include embedded Processing applets and KML output for viewing in Google Earth or any other virtual globe software capable of reading the format.

A tutorial on using SPREAD is availiable here

SUPPORT & LINKS

SPREAD: www.phylogeography.org/SPREAD
Processing libraries: http://processing.org/

Suggestions or report bugs:

<filip.bielejec(sorry_spybots)rega.kuleuven.be>

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

TODO

  • Add main methods to KML templates taking arguments on command line
  • Find a way to get consistent behaviour across non Oracle/Syn JREs (currently OpenJDK shows some weird behaviour when dealing with Processing canvas embedded inside scroll panes).
  • Processing templates: collect data into layers, only then run the AnimationThread, much like it’s currently done in KML templates This way AnimationThread Exceptions will never occur and we don’t have to catch them.
  • Add cannot impute, no precision attribute warning message in Time Slicer.