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, 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, the population
parameter theta based on various approaches, nucleotide diversity,
generalized skyline plots, estimation of absolute evolutionary rates
and clock-like trees using mean path lengths, non-parametric rate
smoothing and penalized likelihood, classifying genes in trees using
the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done
with the NJ, BIONJ, ME, and ML methods.