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(* = Graphable)



Encyclopedia > Nexus file

This bioinformatics-related article is a stub. You can help Wikipedia by expanding it. Map of the human X chromosome (from the NCBI website). ...

Nexus file format is widely used in Bioinformatics. Several popular phoylogenetic programs such as Paup and MacClade use this format. Map of the human X chromosome (from the NCBI website). ...



Command inside square breaket [ and ] are ignored (comment).

Each block start with

 BEGIN block_name; 

and finish with


Basic blocks

  • TAXA block

The TAXA block contains information about taxa.

  • CHARACTER block

The CHARACTER block contains information about the data matrix.

  • DATA block

The DATA block contains the data matrix (e.g. sequence alignment).


  • SETS block;
  • TREES block
  • CODONS block
  • DISTANCES block
  • PAUP block

This block contains all the commands used by Paup*. Please refer to Command Reference Document - Second Draft for detail describtion of each command (PDF format).



  • Maddison, D. R., Swofford, D. L., Maddison, W. P. NEXUS: An extensible file format for systematic information. Systematic Biology 46(4) 1997, 590-621.
  • PAUP* :Phylogenetic Analysis Using Parsimony *and other methods
  • MacClade



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