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 Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Bioequivalence: Overview01:16

Bioequivalence: Overview

Pharmaceutical equivalents, by definition, are drug products with the same active ingredient in the same quantities, encapsulated in identical dosage forms, and intended for the same administration routes. These pharmaceutical equivalents are deemed bioequivalent if the bioavailability of the active entity in the drug preparations is similar. Moreover, pharmaceutical equivalents demonstrating bioequivalence are also regarded as therapeutically equivalent. This means that when used as directed,...
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

You might also read

Related Articles

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

Sort by
Same author

Pediatric Endoscopic Skull Base Surgery: Safety, Efficacy, and Lessons Learned.

Journal of neurological surgery. Part B, Skull base·2026
Same author

CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants.

Briefings in bioinformatics·2026
Same author

Molecular arms race classifier for decrypting venom peptide and ion channel interactions.

Digital discovery·2026
Same author

The wild, wild west of plasmids: First insights into comparative genomics of Borrelia burgdorferi sensu lato.

PloS one·2026
Same author

A ROS-responsive core-shell microneedle platform integrating sonodynamic gas antibacterial therapy and modulating immunity for diabetic wound healing.

Journal of nanobiotechnology·2026
Same author

Germline-targeted baboon apolipoprotein L-1 protects mice against African trypanosomes.

Proceedings of the National Academy of Sciences of the United States of America·2026

Related Experiment Video

Updated: Jul 14, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data.

Thomas Hladish1, Vivek Gopalan, Chengzhi Liang

  • 1Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA. tjhladish@mail.utexas.edu <tjhladish@mail.utexas.edu>

BMC Bioinformatics
|June 15, 2007
PubMed
Summary

Bio::NEXUS is a Perl API simplifying the use of NEXUS files for evolutionary analysis. It offers an object-oriented interface for manipulating genomic data and evolutionary trees, enhancing bioinformatics workflows.

More Related Videos

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Related Experiment Videos

Last Updated: Jul 14, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Area of Science:

  • Bioinformatics and Computational Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Evolutionary analysis utilizes comparative methods for genomic data, treating observations as evolved character states on phylogenetic trees.
  • The NEXUS standard offers a flexible format for character-state data and trees but suffers from complexity and limited software support.
  • This complexity hinders accessibility for bioinformatics users and developers.

Purpose of the Study:

  • To develop a user-friendly Application Programming Interface (API) for the NEXUS file format.
  • To facilitate easier reading, writing, and manipulation of NEXUS files in bioinformatics research.
  • To enhance the integration of NEXUS-formatted data with existing bioinformatics tools and software.

Main Methods:

  • Implementation of an object-oriented API in Perl, named Bio::NEXUS.
  • Development of 22 modules with 351 methods and extensive documentation (POD).
  • Adherence to the NEXUS format as described by Maddison et al., with extensions like NHX tree format support.

Main Results:

  • Bio::NEXUS provides an object-oriented interface for managing NEXUS file contents.
  • The API includes methods for common manipulations such as tree re-rooting and data subset selection.
  • The software is available through CPAN and SourceForge.

Conclusions:

  • Despite NEXUS format complexities, Bio::NEXUS offers a valuable, user-friendly API for its continued utility.
  • Bio::NEXUS functions as "glue code" for connecting diverse software or as a foundation for new applications.
  • The API enhances accessibility and manipulation of evolutionary data in bioinformatics.