Nexus file


The extensible NEXUS file format is widely used in bioinformatics. It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc. Several popular phylogenetic programs such as PAUP*, MrBayes, Mesquite,, MacClade and SplitsTree 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. Comments are enclosed inside square brackets.
There are a few pre-defined block names for common types of data. Examples include:
;TAXA block : The TAXA block contains information about taxa.
;DATA block : The DATA block contains the data matrix.
;TREES block : The TREES block contains phylogenetic trees described using the Newick format, e.g. ;:
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
'
SpaceDog
SpaceCat
SpaceOrc '
SpaceElf
;
End;
BEGIN TREES;
Tree tree1 = ;
END;