Nexus file

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
The TAXA block contains information about taxa.
 * TAXA block

The CHARACTER block contains information about the data matrix.
 * CHARACTER block

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

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

Paup

 * ASSUMPTIONS block
 * SETS block;
 * TREES block
 * CODONS block
 * DISTANCES 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).
 * PAUP block