Analyses of Phylogenetics and Evolution
Description
ape 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,
minimum spanning tree, 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.