Nexus file

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Template:Bioinformatics-stub

Nexus file format is widely used in Bioinformatics. Several popular phoylogenetic programs such as Paup* and MacClade use this format.


Syntax

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

Each block start with

BEGIN block_name; 

and finish with

END;


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).

  • TREES block

The TREES block contains phylogenetic trees described using parenthetical statements, e.g. ((A,B),C);

Paup

  • ASSUMPTIONS block
  • 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).


MacClade

References


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