• ape
  Authors Screenshots History FAQ
• Installation
  Linux Unix Macintosh Windows Updating (all OSs) Stable and Testing Versions
• Literature
  Documentation Citations Analysis of Phylogenetics and Evolution with R
• Development
• pegas
• Links

Development

• Some time ago, I posted some code to visualize trees in ape: it is here.
  
  
• The following document explains how trees are coded in R, and how this data structure can be passed into C.
  
  Definition of Formats for Coding Phylogenetic Trees in R [PDF]
  
  
• The coding scheme used in ape to code DNA sequences is explained in the next document. Its aim is to provide fast algorithms and efficient programs for comparing sequences:
  
  A Bit-Level Coding Scheme for Nucleotides [HTML] [PDF]
  
  
• The following document describes the class "bitsplits" for coding splits of taxa [DRAFT]:
  
  Definition of the Class "bitsplits" [PDF]
  
  
• The application programmers interface (API) to ape C code (THIS IS OUTDATED AND IS HERE ONLY FOR THE RECORD):
  
  The API to ape C code [HTML] [PDF]