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:

#NEXUS Begin data; Dimensions ntax=4 nchar=15; Format datatype=dna missing=? gap=-; Matrix Species1 atgctagctagctcg Species2 atgcta??tag-tag Species3 atgttagctag-tgg Species4 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);: #NEXUS BEGIN TAXA; TAXLABELS A B C; END; BEGIN TREES; TREE tree1 = ((A,B),C); END;