Nexus file

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For the NeXus format used in neutron, x-ray, and muon scattering, see Nexus (data format).

Nexus file format[1] (usually .nex or .nxs) is widely used in Bioinformatics. Several popular phylogenetic programs such as Paup*,[2] MrBayes,[3] Mesquite, and MacClade[4] use this format.

Syntax[edit]

Command inside square brackets [ and ] are ignored (comment). Each block starts with BEGIN block_name; and finishes with END;[5]

An example for a simple DNA alignment would be:

#NEXUS
Begin data;
Dimensions ntax=4 nchar=15;
Format datatype=dna symbols="ACTG" missing=? gap=-;
Matrix
Species1   atgctagctagctcg
Species2   atgcta??tag-tag
Species3   atgttagctag-tgg
Species4   atgttagctag-tag           
;
End;

Basic blocks[edit]

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 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[edit]

References[edit]

  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. ^ MyBayes
  4. ^ MacClade
  5. ^ Detailed NEXUS specification

External links[edit]