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Spatial Phylogenetic Reconstruction of Evolutionary Dynamics

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===== .:: SPREAD ::. =====
Spatial Phylogenetic Reconstruction of Evolutionary Dynamics
Version: 1.0.7rc, 2013
Authors: Filip Bielejec, Andrew Rambaut, Marc A. Suchard & Philippe Lemey
Homepage: www.phylogeography.org
License: LGPL

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 bug reports:

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

COMPILING

Depends on the following libraries:

  • jebl.jar
  • core.jar
  • colt.jar
  • quaqua.jar (libquaqua64.jnilib, libquaqua.jnilib)

CONTRIBUTING

You’re interested in contributing to SPREAD? THAT’S AWESOME! Here are the basic steps:

1. fork SPREAD from here: http://github.com/phylogeography/SPREAD
2. Hack, hack, hack!
3. Document your changes in the Changelog
5. Push the changes
6. Send a pull request to the phylogeography/SPREAD project.

TODO

  • 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
  • Spread v2.0
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