Analysis of Phylogenetics and Evolution

NEW ape 3.0 has been released.
See the list of new features and bug fixes here.

NEW With the release of R 2.14.0, I recommend to re-install ape with "byte-compile" for a substantial increase in performance. This is not the default; for instance under Linux:

R CMD INSTALL --byte-compile ape_3.0.tar.gz

See the manual "R Installation and Administration" (sect. 6.3.5).

About ape

  • ape is a package for the analysis of phylogenetics and evolution.
  • ape is not a classical software (i.e., a "black box" though it can be used as one) but an environment for data analyses and development of new methods where interactivity and user's decisions are left an important place.
  • ape is written in R, but some functions for computer-intensive tasks are written in C.
  • ape is available for all main computer operating systems (Linux, Unix, Windows, MacOS X 10.4 and later).
  • ape is distributed under the terms of the GNU General Public Licence, meaning that it is free and can be freely modified and redistribued (under some conditions).
The SVN repository for ape:
https://svn.mlp.ird.fr/ape/

The "R special interest group on phylogenetic and comparative methods and analyses" mailinglist (thanks to the effort of people in NESCent):
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
All materials on this page are coyrighted:
© Emmanuel Paradis, 2012, except IRD logo © IRD