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Related Concept Videos

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...
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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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...
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...

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Related Experiment Video

Updated: Jun 2, 2026

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

Published on: July 11, 2025

CDAO-store: ontology-driven data integration for phylogenetic analysis.

Brandon Chisham1, Ben Wright, Trung Le

  • 1Department of Computer Science, New Mexico State University, Las Cruces, USA.

BMC Bioinformatics
|April 19, 2011
PubMed
Summary
This summary is machine-generated.

The Comparative Data Analysis Ontology (CDAO) provides semantic descriptions for phylogenetic analysis data. CDAO-Store, a triple-store built using CDAO, offers advanced querying and visualization for phylogenetic trees and data.

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The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: Jun 2, 2026

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

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • The Comparative Data Analysis Ontology (CDAO) was developed to semantically describe data and transformations in phylogenetic analysis.
  • Its core concepts facilitate the description of phylogenetic trees and associated character data matrices.

Purpose of the Study:

  • To develop a semantic backend for phylogenetic data analysis using CDAO.
  • To create a data repository with advanced querying and visualization capabilities for phylogenetic information.

Main Methods:

  • Developed CDAO-Store, a RDF-based triple-store utilizing CDAO as its semantic backend.
  • Integrated a complete import of TreeBASE into CDAO-Store.
  • Implemented web services for programmatic access and a web-based front-end for user interaction.
  • Developed CDAO-Explorer for visualizing character data matrices and phylogenetic trees.

Main Results:

  • CDAO-Store successfully stores and manages phylogenetic data, including imported TreeBASE content.
  • The system supports both user-defined and domain-specific queries (e.g., nearest common ancestors, clade searches, filtering by metadata).
  • CDAO-Explorer enables visualization of data matrices and trees directly from the store.
  • Import capabilities for PHYLIP, MEGA, nexml, and NEXUS formats were established.

Conclusions:

  • CDAO-Store provides a versatile, integrated toolset for phylogenetic analysis.
  • It is the first semantically-aware repository for phylogenetic data offering domain-specific querying.
  • The CDAO-Store portal is accessible for researchers to utilize its functionalities.