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 non-parametric rate smoothing, conversion
of APE trees to and from hclust objects and for classifying genes in
trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation
can be done with the NJ and ML methods.