Lagrange is a Python package implementing likelihood models for geographic range evolution on phylogenetic trees, with methods for inferring rates of dispersal and local extinction and ancestral ranges.

This software implements methods described in Ree, R H and S A Smith. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57(1):4-14.

See also Ree, R H, B R Moore, C O Webb, and M J Donoghue. 2005. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59(11):2299-2311

Analyses are run as Python scripts that use the Lagrange API. Update 23 March 2009: a web-based configuration tool is now available for testing at http://www.reelab.net/lagrange. This tool lets you configure and download your analysis as a Python script which is then run on your own computer. The script therefore requires you to install the latest snapshot release of Lagrange and its dependencies (see System Requirements below).

For help running Lagrange, contact Rick Ree or Stephen Smith.

System requirements

• Python 2.4 or newer
• Scipy - scientific libraries for python (and numpy - numerical libraries)
• for Debian Linux and derivatives, e.g. Ubuntu:

sudo apt-get install python-scipy

• for Mac OS X: see the InstallationMac page
• for Windows: installers available from Sourceforge
• The Enthought Python Distribution bundles scipy, numpy, and many other libraries and is available for Windows, Mac, and Linux

C++ update (July 16, 2010)

There is a BETA binary (executable) of the c++ version of lagrange (same method just different language for speed and some new analyses) in the downloads section. AFTER DOWNLOADING AND UNARCHIVING, run chmod +x lagrange_cpp and it should work if you are running 10.6 MacOSX. There will eventually be BETA's for Linux (though source is easier for Linux users so see below) and MacOSX 10.5 soon. If you would like to compile from source get the source from github (the line is git://github.com/blackrim/lagrange.git) and get one of the BETA executables and follow the instructions in the manual. All the updated info and releases will be here just my development code is hosted on github -- so unless you are diving into the code, stay here for information on lagrange.