Ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel's test, computation of minimum spanning tree, or the population parameter theta based on various approaches. The package is installed in the "/usr/software/ape/ape/R" directory

References:
Emmanuel Paradis is the maintainer for this package, and her homepage can be found here

A PDF Manual for Ape can be found here