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. Phylogeny estimation can be done with the NJ,
BIONJ, and ME methods.