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

Phylogenetic Trees03:21

Phylogenetic Trees

51.4K
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.
51.4K
Phylogenetic Trees03:21

Phylogenetic Trees

6.7K
6.7K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
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...
7.2K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

812
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...
812
Phylogeny01:23

Phylogeny

64.3K
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.
64.3K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

8.3K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
8.3K

You might also read

Related Articles

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

Sort by
Same author

AI-Assisted Detection of Supraspinatus Tendon Pathologies Using a Hierarchical Deep Learning Model to Improve Clinical Applicability: Development and Evaluation Study.

JMIR medical informatics·2026
Same author

Clinical implementation of 3D deep learning techniques in predicting touch-up lesions for atrial fibrillation patients undergoing cryoablation.

International journal of cardiology. Heart & vasculature·2026
Same author

Digital Twins for Predictive Modelling of Thrombosis and Stroke Risk: Current Approaches and Future Directions.

Thrombosis and haemostasis·2026
Same author

Assessing the Evolution and Influence of Medical Open Databases on Biomedical Research and Health Care Innovation: A 25-Year Perspective With a Focus on Privacy and Privacy-Enhancing Technologies.

Journal of medical Internet research·2026
Same author

Echocardiographic Evaluation in Children with Post-Acute Sequelae of SARS-CoV-2 Infection Using Deep Learning.

Journal of imaging informatics in medicine·2026
Same author

Artificial Intelligence Applications in the Diagnosis, Treatment, and Prognosis of Hepatocellular Carcinoma.

Gut and liver·2025

Related Experiment Video

Updated: Mar 13, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K

Phylogenetic tree construction using trinucleotide usage profile (TUP).

Si Chen1, Lih-Yuan Deng2, Dale Bowman2

  • 1Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and School of Pharmaceutical Sciences Wuhan University, Wuhan, China.

BMC Bioinformatics
|October 22, 2016
PubMed
Summary
This summary is machine-generated.

A new Trinucleotide Usage Profile (TUP) method simplifies phylogenetic tree construction using short DNA sequences. TUP offers more biologically supported trees than the feature frequency profile (FFP) method.

Keywords:
Feature frequency profile (FFP)Phylogenetic tree constructionReading frameSummary statisticsTree comparison

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

730
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

11.0K

Related Experiment Videos

Last Updated: Mar 13, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K
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

730
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

11.0K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Constructing genome-wide phylogenetic trees for numerous species with extensive gene sequences presents significant challenges.
  • The established Feature Frequency Profile (FFP-k) method analyzes word frequencies (k-mers) across genome sequences, requiring large computational resources for optimal word lengths (k=6-15).

Purpose of the Study:

  • To introduce a more efficient and biologically accurate method for phylogenetic tree construction.
  • To address the limitations of the FFP-k method in handling large genomic datasets.

Main Methods:

  • Proposed the Trinucleotide Usage Profile (TUP) method, utilizing non-overlapping trinucleotide (3-base word) frequencies.
  • Represented each species using a TUP vector derived from a matrix of three reading frames.
  • Employed distance measures between TUP vectors for phylogenetic tree construction.

Main Results:

  • The TUP method requires significantly fewer possible words (4^3=64) compared to FFP-k.
  • Empirical studies demonstrated that TUP yields phylogenetic trees with stronger biological support than FFP-k.
  • A numerical measure was developed for comparing trees constructed using different methods.

Conclusions:

  • The TUP method offers a more biologically supported approach to phylogenetic tree construction compared to FFP-k.
  • TUP leverages known reading frame start sites, avoiding the information dilution inherent in FFP-k's overlapping word analysis.
  • Information theory analysis supports TUP's enhanced accuracy in gene classification and phylogenetic inference.