| Nexus format | |
| Noextcode: | on |
| Extensions: | usually or |
| Nomimecode: | on |
| Developer: | Maddison DR, Swofford DL, Maddison WP |
| Genre: | bioinformatics |
| Open: | Yes |
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.[1] Several popular phylogenetic programs such as PAUP*,[2] MrBayes,[3] Mesquite,[4] MacClade[5] and SplitsTree[6] use this format.
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]
There are a few pre-defined block names for common types of data. Examples include:[7]
((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;