The primary reference for the use of ape is given by its man (help) pages available in different formats:
You can find the list of all the references cited in the various help pages HERE.
- text from R (?read.tree, ?dist.dna, ...);
- HTML pages browsable from R after typing help.start();
- a PDF manual (ca. 270 pages) available from CRAN here.
For a broader perspective on ape and some other R packages, see Analysis of Phylogenetics and Evolution with R.
For some documentation on the data structures used by ape, see the Development page.
Updated: March 5, 2012
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