First and foremost, thanks to the developers of phylogeny inference programs with which Zephyr can communicate.

Thanks to members of our labs for helping improve Zephyr over the years by making suggestions or finding bugs. We'd like to single out Kojun Kanda for his many good ideas. Kipling Will was especially helpful with the development of the TNT modules, and with general testing of Zephyr on Windows computers. We also thank Mark Miller and Terri Schwartz for their help with CIPRes.

Zephyr was developed in part through funds from the National Science Foundation grant DEB 1258220 to DRM.