Nexus file
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The extensible NEXUS file format is widely used in phylogenetics, evolutionary biology, and bioinformatics. It stores information about taxa, morphological character states, DNA and protein sequence alignments, distances, and phylogenetic trees.[1] 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*,[2] MrBayes,[3] Mesquite,[4] MacClade,[5] and SplitsTree,[6] 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 [...].[7] Each of the pre-defined types of blocks may appear only once.
| Block Name | Description |
|---|---|
| TAXA | Specifies the OTUs (operational taxonomic units) in data set |
| CHARACTERS | Specifies the character data (e.g., homologous morphological characters or a multiple sequence alignment) |
| DATA | Equivalent to a CHARACTERS block that includes the NewTaxa subcommand in the Dimensions command
|
| TREES | Stores trees in Newick format |
| DISTANCES | Stores distance matrices |
| SETS | Assigns names to sets of characters (CHARSET) or OTUs (TAXSET) |
| ASSUMPTIONS | Assumptions about the data or directions regarding data treatment (e.g., the character exclusion status) |
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 Template:DNA sequence
Beta Template:DNA sequence
Gamma Template:DNA sequence [ same as atgttagctag-tgg ]
Delta Template:DNA sequence
;
End;
Begin TREES;
Tree tree1 = ((Alpha,Beta),Gamma,Delta);
END;
See also
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 converter
- NeXML
- Nexus to Fasta converter
- ↑ Script error: No such module "Citation/CS1".
- ↑ PAUP* Template:Webarchive — Phylogenetic Analysis Using Parsimony *and other methods
- ↑ MrBayes
- ↑ Mesquite: A modular system for evolutionary analysis
- ↑ MacClade
- ↑ 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
- ↑ Detailed NEXUS specification