APE 3.3 – Analysis of Phylogenetics and Evolution

APE 3.3


APE (Analysis of Phylogenetics and Evolution) is a package for the analysis of phylogenetics and evolution.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, 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.


APE Team







Bioinformatics. 2012 Jun 1;28(11):1536-7. doi: 10.1093/bioinformatics/bts184. Epub 2012 Apr 11.
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.
Popescu AA1, Huber KT, Paradis E.

Paradis E., Claude J. & Strimmer K. 2004.
APE: analyses of phylogenetics and evolution in R language.
Bioinformatics 20: 289–290.