• ape
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• Installation
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• Literature
  Documentation Citations Analysis of Phylogenetics and Evolution with R
• Development
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Development

• 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" coding splits of taxa [DRAFT]:
  
  Definition of the Class "bitsplits" [PDF]
  
  
• The application programmers interface (API) to ape C code:
  
  The API to ape C code [HTML] [PDF]