Nexus file

Syntax

Command inside square brackets [ and ] are ignored (comment). Each block starts with BEGIN block_name; and finishes with END;

An example for a simple DNA alignment would be:

#NEXUSBegin data;Dimensions ntax=4 nchar=15;Format datatype=dna missing=? gap=-;MatrixSpecies1 atgctagctagctcgSpecies2 atgcta??tag-tagSpecies3 atgttagctag-tggSpecies4 atgttagctag-tag ;End;

Basic blocks

TAXA block 

The TAXA block contains information about taxa.

DATA block 

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

TREES block 

The TREES block contains phylogenetic trees described using the Newick format, e.g. ((A,B),C);:#NEXUSBEGIN TAXA; TAXLABELS A B C;END;BEGIN TREES; TREE tree1 = ((A,B),C);END;