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Nexus: An Extensible File Format for Systematic Information
Open accessAbstract
NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.; private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.
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Citations
Cited by
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Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
Multiple sequence alignment with the Clustal series of programs
Chenna, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg500 · Cited by 4,875
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
Metadata
- Authors
- Maddison, D. R., Swofford, D. L., & Maddison, W. P.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-12-01
- Volume
- 46
- Issue
- 4
- Pages
- 590-621
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2100412820
- Cited by
- 519
- References
- 0
- FWCI
- 2.14
- Type
- journal article
- Language
- en
- Open access
- bronze
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- CoChat. (2026). Citation check: Nexus: An Extensible File Format for Systematic Information. https://app.cochat.ai/papers/10.1093/sysbio/46.4.590
- The paper
- Maddison, D. R., Swofford, D. L., & Maddison, W. P. (1997). Nexus: An Extensible File Format for Systematic Information. Systematic Biology. https://doi.org/10.1093/sysbio/46.4.590
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
