Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

NEXUS: an extensible file format for systematic information.

D R Maddison1, D L Swofford, W P Maddison

  • 1Department of Entomology, University of Arizona, Tucson, Arizona 85721, USA. beetle@ag.arizona.edu

Systematic Biology
|April 27, 2002
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Loss of genetic variability in social spiders: genetic and phylogenetic consequences of population subdivision and inbreeding.

Journal of evolutionary biology·2012
Same author

Complete separation along matrilines in a social spider metapopulation inferred from hypervariable mitochondrial DNA region.

Molecular ecology·2010
Same author

Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae).

Zoologica scripta·2009
Same author

Sequence alignment of 18S ribosomal RNA and the basal relationships of Adephagan beetles: evidence for monophyly of aquatic families and the placement of Trachypachidae.

Systematic biology·2002
Same author

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods.

Systematic biology·2002
Same author

Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?

Systematic biology·2002
Same journal

Diversification dynamics in the global radiation of gobies.

Systematic biology·2026
Same journal

Correction to: nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Systematic biology·2026
Same journal

Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae).

Systematic biology·2026
Same journal

An evolving view of phylogenetic biogeography.

Systematic biology·2026
Same journal

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026
Same journal

Coalescent-based branch length estimation improves dating of species trees.

Systematic biology·2026
See all related articles

The NEXUS file format provides a modular and extensible system for storing systematic biological data. It ensures cross-platform compatibility and ease of processing for various computational biology programs.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systematic Data Management

Background:

  • Systematic data is crucial for computational biology and bioinformatics.
  • Existing data formats may lack flexibility, cross-platform compatibility, or extensibility.
  • A standardized format is needed for efficient data exchange and analysis.

Purpose of the Study:

  • To introduce the NEXUS file format for systematic data.
  • To outline the design goals of NEXUS, including modularity, extensibility, and platform independence.
  • To provide guidelines for using and extending the NEXUS format.

Main Methods:

  • NEXUS employs a modular structure with distinct blocks for specific data types.
  • Standardized commands facilitate program processing.

Related Experiment Videos

  • Public blocks store common data (taxa, characters, trees), while private blocks are program-specific.

    • Main Results:

    • The NEXUS format is detailed, including its modular design and command structure.
    • Guidelines for reading, writing, and extending NEXUS files are provided.
    • The format supports diverse systematic data, including morphological and molecular characters, and phylogenetic trees.

    Conclusions:

    • NEXUS offers a robust and flexible file format for systematic data in computational biology.
    • Its modular and extensible design ensures long-term usability and broad applicability.
    • NEXUS facilitates data sharing and analysis across different software and operating systems.