Nexus (bioinformatics)

from Wikipedia, the free encyclopedia

The Nexus format is a widely used file format in systematic biology and bioinformatics that is used in several computer programs for family tree analysis .

syntax

Nexus files are text files that have a modular format: in addition to mandatory blocks, optional blocks can contain information and commands for specific applications. Each block begins with the line BEGIN BlockName;and ends with the line END;. Sense sections within a block are also ;separated. Text between square brackets is treated as a comment and is therefore ignored. The first line must be #NEXUS.

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

#NEXUS
BEGIN data;[eröffnet den "Data"-Block]
Dimensions ntax=4 nchar=15; [Definiert die Größe des Alignments]
Format datatype=dna missing=? gap=-; [Definiert den Datentyp (DNA) und Symbole für fehlende Daten (?) und gaps (-)]
Matrix [hier beginnt das Alignment...]
Species1   atgctagctagctcg
Species2   atgcta??tag-tag
Species3   atgttagctag-tgg
Species4   atgttagctag-tag 
; [...und hier endet es]
END; [beendet den "Data"-Block]

swell

  • Maddison DR, Swofford DL, Maddison WP: NEXUS: An extensible file format for systematic information . In: Systematic Biology . tape 46 , no. 4 , 1997, p. 590-621 , doi : 10.1093 / sysbio / 46.4.590 .
  • Detailed article about the NEXUS format with a list of key words