APE home page

Features

Generalities
ape's Philosophy
Methods Available
Future Developments

Generalities

ape can be used at several levels:

for traditional analyses and tree drawing with many high-level functions;
for exploratory analyses of your data using the utility functions to manipulate trees or extract various informations, and all R functions;
development of new methods with R programs or possibly interfacing C, C++, Fortran.

ape provides methods for the analysis of phylogenies at the interspecific levels. At the moment, it deals mainly with analyses of reconstructed phylogenies (analysis of diversification, phylogenetic comparative analyses, and ancestral character estimation), and tree drawing. But current developments are undertaken to provide functions for phylogeny estimation, though distance-based methods are already available (UPGMA, NJ, BIONJ, and ME).

ape is an R package: this means that you need to have R installed on your computer to use ape. If this isn't already done, do yourself a favour today: download and install R!

There are other projects similar to ape (in alphabetical order):

ade4 (analyses des données écologiques) by Daniel Chessel, Anne-Béatrice Dufour and Stéphane Dray, with contributions from Jean Lobry, Sébastien Ollier, Sandrine Pavoine and Jean Thioulouse;
adephylo by Thibaut Jombart;
seqinr (sequences in R) by Delphine Charif and Jean Lobry.

Other packages are available on CRAN and can found through the TaskView page on Genetics and the one on Phylogenetics. Several packages are also available on R-Forge in the Phylogenetics subtopic

Because ape's data structures have become an implicit standard over the years, a good way to check-out the new packages is to look at those that depend on it (see bottom of this page).

The package dna by Jim Lindsey includes a port of Clustal W and flip; it can be downloaded from his web site.

ape's Philosophy

The ideas driving the development of ape are:

Stick to R's logic as much as possible.
Search for efficiency in the code at all levels.
Broad integration of methods for the analysis of evolutionary processes.
Provide tools for the widest range of users.

Methods Available

Roughly, the methods in ape can be grouped in seven categories:

Reading/writing phylogenetic trees
Manipulating phylogenetic trees (including analysis of bipartitions, tree comparisons, ...)
Reading/writing DNA sequences
Computing distances from DNA sequences
Phylogenetic comparative methods
Estimation of ancestral characters
Analysis of diversification

Three further categories can be added where developments are currently active:

Estimation of phylogenetic trees
Molecular dating
Analysis of population genetic history

A complete description of the ape functions can be found in the ape Manual [PDF 930 KB].

Future Developments

ape is in continuous development (for the amateurs of circular acronyms, APE could stand for "Ape is a Package in Evolution"). A strength of ape is in the analysis of reconstructed phylogenies, and the effort will be carried on in this direction.

The best way to keep track of the news about ape is to check-out regularly the present web site, and stay tuned on the r-sig-phylo mailing list.