Nexus file
For the NeXus format used in neutron, x-ray, and muon scattering, see Nexus (data format).
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
References
- ↑ 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.
- ↑ PAUP* — Phylogenetic Analysis Using Parsimony *and other methods
- ↑ MrBayes
- ↑ Mesquite: A modular system for evolutionary analysis
- ↑ MacClade
- ↑ 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
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