The extensible NEXUS file format is widely used in
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
. It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.
Several popular phylogenetic programs such as
PAUP*
PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (Phylogenetics, phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implem ...
,
[PAUP*](_blank)
— Phylogenetic Analysis Using Parsimony *and other methods MrBayes
Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood ...
,
[MrBayes](_blank)
/ref> Mesquite,[Mesquite: A modular system for evolutionary analysis](_blank)
/ref> MacClade
/ref> and SplitsTree
SplitsTree is a popular freeware program for inferring phylogenetic trees, phylogenetic networks, or, more generally, splits graphs, from various types of data such as a sequence alignment, a distance matrix or a set of trees. SplitsTree impleme ...
[ 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.
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. Comment
Comment may refer to:
* Comment (linguistics) or rheme, that which is said about the topic (theme) of a sentence
* Bernard Comment (born 1960), Swiss writer and publisher
Computing
* Comment (computer programming), explanatory text or informat ...
s are enclosed inside square brackets .[Detailed NEXUS specification](_blank)
/ref>
There are a few pre-defined block names for common types of data. Examples include:((A,B),C);:
The following example uses the three block types above:
#NEXUS
Begin TAXA;
Dimensions ntax=4;
TaxLabels SpaceDog SpaceCat SpaceOrc SpaceElf;
End;
Begin data;
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. '
SpaceDog
SpaceCat
SpaceOrc '' same as atgttagctag-tgg '
SpaceElf
;
End;
BEGIN TREES;
Tree tree1 = (((SpaceDog,SpaceCat),SpaceOrc,SpaceElf));
END;
See also
* Newick format
*NeXML format
NeXML is an exchange standard for representing phyloinformatic data. It was inspired by the widely used Nexus file format but uses XML to produce a more robust format for rich phylogenetic data. Advantages include syntax validation, semantic anno ...
* phyloXML
*PAUP*
PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (Phylogenetics, phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implem ...
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