Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Phylogenetic Trees

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.

Evolutionary Relationships through Genome Comparisons

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...

Phylogeny

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.

Mutation, Gene Flow, and Genetic Drift

Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).

Applications of Molecular Taxonomy

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...

Types of Genetic Transfer Between Organisms

Types of Genetic Transfer Between Organisms

Genetic transfer occurs when genetic information is passed from one organism to another. It occurs via two mechanisms: vertical gene transfer and horizontal gene transfer. Vertical gene transfer occurs when genetic information is transferred from one generation to the next, which happens much more frequently than horizontal gene transfer. Both sexual and asexual reproduction are forms of vertical gene transfer, where one or more organisms pass some or all of their genome onto their progeny.

You might also read

Related Articles

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

Sort by

Same author

Effect of Mixed Valence Cu-In Bimetallic Oxides on Promoting Electrocatalytic Reduction of CO<sub>2</sub> to CO.

Langmuir : the ACS journal of surfaces and colloids·2026

Same author

<i>Special Issue:</i> 13th International Conference on Computational Advances in Bio and Medical Sciences.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same author

Metabolism-Based Biomarkers for Rapid Phenotypic Antibiotic Susceptibility Testing.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Same author

Gallium in liquid state shows nuclease-mimicking activity.

Nature communications·2026

Same author

The landscape of machine learning approaches for modeling protein conformational ensembles.

Current opinion in structural biology·2026

Same author

Reticuline isomerase AKR1B1 with aldo-keto reductase activity and detoxification function from the insect Blaps rhynchopetera.

International journal of biological macromolecules·2026

Search research articles

Related Experiment Video

Updated: Nov 14, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference.

Samuel Sledzieski¹, Chengchen Zhang, Ion Mandoiu

¹Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

|March 10, 2021

Summary

TreeFix-TP accurately reconstructs infectious disease transmission phylogenies by correcting errors in evolutionary history. This improves outbreak source detection and network inference, even for large-scale epidemics.

More Related Videos

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

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

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

Published on: July 11, 2025

Related Experiment Videos

Last Updated: Nov 14, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

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

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

Published on: July 11, 2025

Area of Science:

Epidemiology
Computational Biology
Evolutionary Biology

Background:

Infectious disease transmission network inference relies on accurate phylogenetic reconstruction.
Existing phylogenetic methods can be error-prone and do not scale well for large outbreaks, hindering transmission network analysis.

Purpose of the Study:

To introduce TreeFix-TP, a novel method for accurate and scalable reconstruction of transmission phylogenies.
To improve the accuracy of phylogenetic inference for infectious disease outbreaks.

Main Methods:

TreeFix-TP employs an error-correction framework, integrating intra-host diversity and host information.
It balances parsimonious transmission network evaluation with statistical hypothesis testing on sequence data likelihood.
The method reconstructs trees that minimize transmissions while maintaining high sequence data support.

Main Results:

TreeFix-TP demonstrated improved phylogenetic accuracy in simulations of viral transmission and evolution.
The method enhanced outbreak source detection using real-world Hepatitis C Virus (HCV) outbreak data.
Performance remained robust across various transmission and evolutionary parameters.

Conclusions:

TreeFix-TP significantly enhances transmission phylogeny inference and outbreak source detection.
The method offers a scalable and accurate solution for analyzing infectious disease transmission networks.
Open-source availability facilitates broader application in epidemiological studies.