The code within should be functional and steps followed during data collection and analysis are available from:

• https://gist.github.com/47e03463db0573c4252f

These steps generally apply to the computer code within this repository. However, pathnames within the notes are unlikely to be equivalent to pathnames on your system.

To generate species trees from gene trees, we used:

• https://github.com/ngcrawford/CloudForest

This list may not be complete.

• Biopython
• bx-python
• numpy

• Jim Kent Source Tree
• mraic_mod.pl

If you use portions of this code in your own work, please contact the author(s) to ensure there is not a newer, officially packaged version. If there is not, please cite the following manuscript:

Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC: Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. Systematic Biol. 2012.