The extensible NEXUS file format is widely used in
phylogenetics
In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...
, evolutionary biology, and
bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
. It stores information about
taxa
In biology, a taxon (back-formation from ''taxonomy''; : taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and ...
, morphological character states, DNA and protein sequence alignments, distances, and phylogenetic trees.
The NEXUS format also allows the storage of data that can facilitate analyses, such as sets of characters or taxa. Many popular phylogenetic programs, including
PAUP*,
[PAUP*](_blank)
— Phylogenetic Analysis Using Parsimony *and other methods MrBayes,
[MrBayes](_blank)
/ref> Mesquite,[Mesquite: A modular system for evolutionary analysis](_blank)
/ref> MacClade,
/ref> and SplitsTree,[ Huson and Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Mol Biol Evol (2005) 23 (2): 254-267. https://doi.org/10.1093/molbev/msj030] use this format. Nexus file names typically have the extension .nxs or .nex .
Syntax
A NEXUS file is made out of a fixed header #NEXUS followed by multiple blocks. Each block starts with BEGIN block_name; and ends with END;. The keywords are case-insensitive. Comments are enclosed inside square brackets .[Detailed NEXUS specification](_blank)
/ref> Each of the pre-defined types of blocks may appear only once.
The following example NEXUS uses the TAXA, CHARACTERS, and TREES blocks:
#NEXUS
Begin TAXA;
Dimensions ntax=4;
TaxLabels Alpha Beta Gamma Delta;
End;
Begin CHARACTERS;
Dimensions nchar=15;
Format datatype=dna missing=? gap=- matchchar=.;
Matrix
When a position is a "matchchar", it means that it is the same as the first entry at the same position. Alpha
Beta
Gamma same as atgttagctag-tgg Delta
;
End;
Begin TREES;
Tree tree1 = ((Alpha,Beta),Gamma,Delta);
END;
See also
* Newick format
* NeXML format
* phyloXML
References
External links
NEXUS file format
— detailed explanation with many examples
NEXUS format
— a good description of the format and its uses in the field
Nexus to phyloXML converterNeXMLNexus to Fasta converter
{{Bioinformatics
Bioinformatics
Biological sequence format
Phylogenetics