Spatial Phylogenetic Reconstruction of Evolutionary Dynamics
Java HTML C Other
Latest commit 8f07a09 Sep 12, 2016 @fbielejec fbielejec committed on GitHub Update and rename README.textile to README.md

README.md

Important This software is no longer actively maintained, users are encouraged to migrate to SpreaD3.

.:: SPREAD ::.

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

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.

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

SUPPORT & LINKS

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

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
  4. Push the changes
  5. Send a pull request to the phylogeography/SPREAD project.

TODO

  • 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