r-cran-ape 3.1-1-1 (i386 binary) in ubuntu utopic

 This package provides functions for reading, writing, plotting, and
 manipulating phylogenetic trees, analyses of comparative data in a
 phylogenetic framework, ancestral character analyses, analyses of
 diversification and macroevolution, computing distances from allelic
 and nucleotide data, reading and writing nucleotide sequences, and
 several tools such as Mantel's test, generalized skyline plots,
 graphical exploration of phylogenetic data (alex, trex, kronoviz),
 estimation of absolute evolutionary rates and clock-like trees using
 mean path lengths and penalized likelihood. Phylogeny estimation can
 be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and
 several methods handling incomplete distance matrices (NJ*, BIONJ*,
 MVR*, and the corresponding triangle method). Some functions call
 external applications (PhyML, Clustal, T-Coffee, Muscle) whose
 results are returned into R.