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 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.
