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

Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

You might also read

Related Articles

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

Sort by
Same author

Genome-based taxonomy and provirus identification in <i>Halococcus</i> from hypersaline environments.

Current research in microbial sciences·2026
Same author

Cryo-EM structure of the native assembled Mfa type V pilus from the periodontal pathogen Porphyromonas gingivalis.

Communications biology·2026
Same author

Screening anxiety via contrastive autobiographical recall.

Frontiers in digital health·2026
Same author

Offset reconstruction in stemless and stemmed shoulder hemiarthroplasty: influence on long-term outcomes.

Archives of orthopaedic and trauma surgery·2026
Same author

Genomic insights into antiviral defense systems in haloarchaea and their impact on virus susceptibility.

Virology·2026
Same author

Cryo-EM in enzymology and dynamics.

Structure (London, England : 1993)·2026

Related Experiment Video

Updated: May 24, 2026

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies.

Christian Koetschan1, Thomas Hackl, Tobias Müller

  • 1Department of Bioinformatics, Biocenter, University Würzburg, Germany.

Molecular Phylogenetics and Evolution
|February 28, 2012
PubMed
Summary

The ITS2 Workbench streamlines molecular phylogenetics by integrating taxon sampling with alignment and tree reconstruction. This tool enables faster, iterative improvements for more accurate phylogenetic analyses using ITS2 sequence data.

More Related Videos

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Related Experiment Videos

Last Updated: May 24, 2026

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenetic analysis relies on accurate taxon sampling, which is often hindered by sequence errors, inaccurate database annotations, and incorrect taxonomic classifications.
  • Current methods often require iterative correction of taxon sampling after phylogenetic tree calculation, leading to time-consuming and tedious processes.
  • The decoupling of taxon sampling from subsequent analysis steps complicates the refinement of datasets for molecular phylogenetics.

Purpose of the Study:

  • To present the ITS2 Workbench, a novel computational tool designed to address the challenges in taxon sampling for molecular phylogenetic analyses.
  • To integrate taxon sampling, secondary structure prediction, multiple alignment, and phylogenetic tree calculation into a cohesive workflow.
  • To enable interactive and iterative refinement of taxon sampling for improved accuracy in ITS2-based phylogenies.

Main Methods:

  • The ITS2 Workbench tightly integrates multiple critical steps of phylogenetic analysis, including taxon sampling, secondary structure prediction, multiple sequence alignment, and phylogenetic tree reconstruction.
  • It leverages the extensive ITS2 database, which provides access to over 280,000 ITS2 sequences and their corresponding secondary structures.
  • The platform facilitates sequence-structure based alignment and tree reconstruction, enabling interactive improvements throughout the process.

Main Results:

  • The ITS2 Workbench successfully integrates taxon sampling with downstream phylogenetic analysis steps, eliminating the need for iterative, de-coupled corrections.
  • The tool provides access to a large dataset of ITS2 sequences and structures, supporting sequence-structure based alignment and tree reconstruction.
  • It enables interactive and iterative refinement of taxon sampling, leading to a more efficient and accurate phylogenetic analysis workflow.

Conclusions:

  • The ITS2 Workbench significantly enhances the accuracy and efficiency of molecular phylogenetic analyses, particularly those utilizing ITS2 markers.
  • By integrating taxon sampling with alignment and tree building, the tool streamlines the entire process, reducing potential errors and saving time.
  • This integrated approach allows for rapid, interactive, and iterative taxon sampling, ultimately leading to more reliable ITS2-based phylogenies.