Nexus file
Filename extensions | usually .nex or .nxs |
---|---|
Internet media type | application/octet-stream |
Magic number | '#NEXUS\n' |
Developed by | Maddison DR, Swofford DL, Maddison WP |
Initial release | December 1997 (26 years ago) (1997-12) |
Type of format | bioinformatics |
Open format? | 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.
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 [...]
.[7]
There are a few pre-defined block names for common types of data. Examples include:[7]
- TAXA block
- The TAXA block contains information about taxa.
- 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);
:
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 atgctagctagctcg SpaceCat ......??...-.a. SpaceOrc ...t.......-.g. [ same as atgttagctag-tgg ] SpaceElf ...t.......-.a. ; End; BEGIN TREES; Tree tree1 = (((SpaceDog,SpaceCat),SpaceOrc,SpaceElf)); END;
See also
- Newick format
- NeXML format
- phyloXML
- PAUP*
References
- ^ 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.
- ^ PAUP* Archived 2006-09-03 at the Wayback Machine — Phylogenetic Analysis Using Parsimony *and other methods
- ^ MrBayes
- ^ Mesquite: A modular system for evolutionary analysis
- ^ MacClade
- ^ Huson and Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Mol Biol Evol (2005) 23 (2): 254-267. https://doi.org/10.1093/molbev/msj030
- ^ a b Detailed NEXUS specification
External links
- NEXUS file format — detailed explanation with many examples
- NEXUS format — a good description of the format and its uses in the field
- Nexus to phyloXML converter
- NeXML
- Nexus to Fasta converter
- v
- t
- e
Bioinformatics
- Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank
- Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
- Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology
- Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network
- Server: ExPASy
- Rosalind (education platform)
- Broad Institute
- Computational Biology Department (CBD)
- Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
- Database Center for Life Science (DBCLS)
- DNA Data Bank of Japan (DDBJ)
- European Bioinformatics Institute (EMBL-EBI)
- European Molecular Biology Laboratory (EMBL)
- Flatiron Institute
- J. Craig Venter Institute (JCVI)
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
- US National Center for Biotechnology Information (NCBI)
- Japanese Institute of Genetics
- Netherlands Bioinformatics Centre (NBIC)
- Philippine Genome Center (PGC)
- Scripps Research
- Swiss Institute of Bioinformatics (SIB)
- Wellcome Sanger Institute
- Whitehead Institute
- African Society for Bioinformatics and Computational Biology (ASBCB)
- Australia Bioinformatics Resource (EMBL-AR)
- European Molecular Biology network (EMBnet)
- International Nucleotide Sequence Database Collaboration (INSDC)
- International Society for Biocuration (ISB)
- International Society for Computational Biology (ISCB)
- Student Council (ISCB-SC)
- Institute of Genomics and Integrative Biology (CSIR-IGIB)
- Japanese Society for Bioinformatics (JSBi)
- Basel Computational Biology Conference ([BC2])
- European Conference on Computational Biology (ECCB)
- Intelligent Systems for Molecular Biology (ISMB)
- International Conference on Bioinformatics (InCoB)
- International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
- ISCB Africa ASBCB Conference on Bioinformatics
- Pacific Symposium on Biocomputing (PSB)
- Research in Computational Molecular Biology (RECOMB)
- CRAM format
- FASTA format
- FASTQ format
- NeXML format
- Nexus format
- Pileup format
- SAM format
- Stockholm format
- VCF format
- GFF format
- Category
- Commons