Nexus file

The NEXUS file format^[1] (usually .nex or .nxs) is widely used in bioinformatics. Several popular phylogenetic programs such as PAUP*,^[2] MrBayes,^[3] Mesquite,^[4] and MacClade^[5] use this format.

Syntax

Command inside square brackets [ and ] are ignored (comment). Each block starts with BEGIN block_name; and finishes with END;^[6]

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;

See also

• Newick format
• NeXML format
• phyloXML

References

1. Maddison DR, Swofford DL, Maddison WP (1997). "NEXUS: An extensible file format for systematic information". Systematic Biology 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335.
2. PAUP* — Phylogenetic Analysis Using Parsimony *and other methods
3. MrBayes
4. Mesquite: A modular system for evolutionary analysis
5. MacClade
6. Detailed NEXUS specification

External links

• NEXUS file format — detailed explanation with lots of examples
• NEXUS format — a good description of the format and its uses in the field
• Nexus to phyloXML converter
• NeXML
• Nexus to Fasta converter