Nexus file

Nexus file
For the NeXus format used in particle physics, see Nexus (data format).

Nexus file format[1] is widely used in Bioinformatics. Several popular phylogenetic programs such as Paup*,[2] MrBayes,[3] Mesquite, and MacClade[4] use this format.

Contents

Syntax

Command inside square brackets [ and ] are ignored (comment). Each block starts with BEGIN block_name; and finishes with END;[5]

An example for a simple DNA alignment would be:

#NEXUS
Begin data;
Dimensions ntax=4 nchar=15;
Format datatype=dna symbols="ACTG" missing=? gap=-;
Matrix
Species1   atgctagctagctcg
Species2   atgcta??tag-tag
Species3   atgttagctag-tgg
Species4   atgttagctag-tag           
;
End;

Basic blocks

TAXA block 
The TAXA block contains information about taxa.
CHARACTER block 
The CHARACTER block contains information about the data matrix.
DATA block 
The DATA block contains the data matrix (e.g. sequence alignment).
TREES block 
The TREES block contains phylogenetic trees described using the Newick format, e.g. ((A,B),C);

Paup

ASSUMPTIONS block
SETS block;
TREES block
CODONS block
DISTANCES block
PAUP block 
This block contains all the commands used by Paup*. (refer to Command Reference Document - Second Draft for detail describtion of each command.)

See also

References

  1. ^ Maddison DR, Swofford DL, Maddison WP (1997). "NEXUS: An extensible file format for systematic information". Systematic Biology 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335. 
  2. ^ PAUP* — Phylogenetic Analysis Using Parsimony *and other methods
  3. ^ MyBayes
  4. ^ MacClade
  5. ^ Detailed NEXUS specification

External links

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