Nexus file

The Nexus format is an in systematic biology and bioinformatics widely used file format that takes place in several computer programs for pedigree analysis application.

Syntax

Nexus files are text files that have a modular format: In addition to mandatory optional blocks blocks may contain information and instructions for specific applications. Each block begins with the line BEGIN block name; and ends with the line END;. Sense sections within a block will also be; separately. Text between square brackets is interpreted as a comment and ignored it. The first line should read # NEXUS.

An example of a simple Nexus file with a sequence alignment is:

# NEXUS BEGIN data; [ opens the "Data " block ] Dimensions NTAX = 4 nchar = 15; [ Defines the size of the alignment ] Format datatype = dna missing =? gap = -; [ Defines the data type (DNA) and symbols for missing data and gaps (?) (-)] Matrix [here begins the alignment ... ] Species1 atgctagctagctcg Species2 atgcta? Tag - tag Species3 atgttagctag - tgg Species4 atgttagctag tag; [ ... and here it ends ] END; [Complete the "Data " block ] swell

  • Maddison DR, Swofford DL, Maddison WP: NEXUS: An extensible file format for systematic information. In: Systematic Biology. 46, No. 4, 1997, pp. 590-621, doi: 10.1093/sysbio/46.4.590.
  • Detailed article on the NEXUS format with a list of keywords (English)
  • Data format
  • Bioinformatics
Indel Digital Object Identifier
600983
de