Package

r-ape

Description

Analyses of Phylogenetics and Evolution. 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 DNA
sequences, reading and writing nucleotide sequences as well as importing
from BioConductor, 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, dating trees
with non-contemporaneous sequences, translating DNA into AA sequences,
and assessing sequence alignments. 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.

Note