The following persons and institutions helped in the development of APE at one stage or another. Many users gave important feed-back with their encouragements, comments, or bug reports: thanks to all of you! Significant bug fixes were provided by Cécile Ané, James Bullard, Éric Durand, Olivier François, Bret Larget, Nick Matzke, Elizabeth Purdom, Dan Rabosky, Klaus Schliep, Li-San Wang, Yan Wong, and Peter Wragg. Contact me if I forgot someone. Kurt Hornik, of the R Core Team, helped in several occasions to fix some problems and bugs. Financial support was provided in the early development of APE by the French "Programme inter-EPST Bioinformatique" (2001-2003). Financial support was provided by the Department of Information Systems of IRD in form a "SPIRALES" project (2006).