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

NCL: a C++ class library for interpreting data files in NEXUS format.

Paul O Lewis1

  • 1Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA. paul.lewis@uconn.edu

Bioinformatics (Oxford, England)
|November 25, 2003
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

LoRaD: Marginal likelihood estimation with haste (but no waste).

Systematic biology·2023
Same author

An experimental test of Lanchester's models of combat in the neotropical termite <i>Nasutitermes corniger</i> (Blattodea: Termitidae).

Proceedings. Biological sciences·2022
Same author

New partition based measures for data compatibility and information gain.

Statistics in medicine·2021
Same author

Dysphagia after Stroke: An Unmet Antibiotic Stewardship Opportunity.

Dysphagia·2021
Same author

An Unusual Case of COVID-19 Presenting as Acute Psychosis.

Journal of pharmacy practice·2020
Same author

Utility of the respiratory viral panel as an antimicrobial stewardship tool.

Journal of clinical pharmacy and therapeutics·2020
Same journal

Probabilistic RNA designability via interpretable ensemble approximation and dynamic decomposition.

Bioinformatics (Oxford, England)·2026
Same journal

Quantifying domain-specific relevance of computational biology Wikipedia articles using TF-IDF and cosine similarity.

Bioinformatics (Oxford, England)·2026
Same journal

GATSBI: improving context-aware protein embeddings through biologically motivated data splits.

Bioinformatics (Oxford, England)·2026
Same journal

BiMba: using Vision Mamba to predict protein sites that bind other proteins.

Bioinformatics (Oxford, England)·2026
Same journal

ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics.

Bioinformatics (Oxford, England)·2026
Same journal

Is a Win-Win possible? Achieving pareto-optimal privacy-utility balance in fine-tuned genome language model embeddings against embedding reconstruction attacks.

Bioinformatics (Oxford, England)·2026
See all related articles

The NEXUS Class Library (NCL) simplifies data interpretation for phylogenetic analyses using the NEXUS format. This C++ library encourages wider adoption of NEXUS by making it easier for developers to integrate NEXUS file compatibility into new software.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • The NEXUS format is widely used in phylogenetic analysis software for data sharing.
  • Current software often has limited ability to interpret all NEXUS data types.
  • Reformatting data for different programs can lead to errors and data duplication.

Purpose of the Study:

  • To develop a C++ library (NCL) to simplify the interpretation of NEXUS data files.
  • To encourage broader adoption and use of the NEXUS format in bioinformatics.
  • To facilitate the integration of NEXUS file compatibility into new phylogenetic software.

Main Methods:

  • The NEXUS Class Library (NCL) provides a collection of C++ classes.
  • NCL is designed to parse and interpret data structured in the NEXUS format.

Related Experiment Videos

  • The library aims to streamline the process for developers adding NEXUS support.

    • Main Results:

    • NCL offers a standardized approach to handling NEXUS data.
    • It reduces the complexity for programmers to implement NEXUS file reading capabilities.
    • The library promotes data integrity by minimizing reformatting needs.

    Conclusions:

    • The NCL enhances the usability of the NEXUS format for phylogenetic analyses.
    • By simplifying data interpretation, NCL supports interoperability between different bioinformatics tools.
    • Widespread use of NCL can lead to more robust and error-free data sharing in evolutionary biology research.