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

Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
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.
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.
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...

You might also read

Related Articles

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

Sort by
Same author

A multi-task domain-adapted model to predict chemotherapy response from mutations in recurrently altered cancer genes.

iScience·2025
Same author

A Joint LLM-KG System for Disease Q&A.

IEEE journal of biomedical and health informatics·2025
Same author

Evaluating Explanations From AI Algorithms for Clinical Decision-Making: A Social Science-Based Approach.

IEEE journal of biomedical and health informatics·2024
Same author

ASTER: A Method to Predict Clinically Relevant Synthetic Lethal Genetic Interactions.

IEEE journal of biomedical and health informatics·2024
Same author

Avoiding inferior clusterings with misspecified Gaussian mixture models.

Scientific reports·2023
Same author

ExpertNet: A Deep Learning Approach to Combined Risk Modeling and Subtyping in Intensive Care Units.

IEEE journal of biomedical and health informatics·2023

Related Experiment Video

Updated: May 19, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Bootstrapping phylogenies inferred from rearrangement data.

Yu Lin1, Vaibhav Rajan, Bernard Me Moret

  • 1Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland. bernard.moret@epfl.ch.

Algorithms for Molecular Biology : AMB
|August 31, 2012
PubMed
Summary

We developed a new nonparametric method to assess phylogenetic trees built from whole-genome rearrangement data. This approach provides reliable support values, similar to the classic bootstrap for sequence data, enabling confident whole-genome phylogenetic analyses.

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

Related Experiment Videos

Last Updated: May 19, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

Area of Science:

  • Genomics and Bioinformatics
  • Computational Evolutionary Biology
  • Phylogenetic Inference

Background:

  • Large-scale genome sequencing facilitates phylogenetic inference using genomic architecture evolution (rearrangements, duplications, losses).
  • Existing phylogenetic assessment methods like bootstrap and jackknife are unsuitable for whole-genome rearrangement data, as genomes are treated as single characters.
  • Lack of established probabilistic models prevents the application of likelihood tests for assessing phylogenies based on genomic rearrangements.

Purpose of the Study:

  • To introduce a novel nonparametric approach for assessing distance-based phylogenetic inference from whole-genome data.
  • To provide a robust method for evaluating phylogenetic trees derived from genomic rearrangements, analogous to the bootstrap for sequence data.

Main Methods:

  • Developed a new nonparametric assessment method combining features of jackknife and bootstrap techniques.
  • Conducted extensive experimental testing comparing the new method with classic bootstrap and other variants in both sequence-based and genome-based frameworks.
  • Validated the approach on a dataset of mammalian genomes to assess support values for phylogenetic branches.

Main Results:

  • The new bootstrapping approach demonstrates performance comparable to the classic phylogenetic bootstrap for sequence-based reconstruction.
  • The proposed method for rearrangement data significantly outperforms existing variants.
  • Support values obtained from the new method on mammalian genomes align with established evolutionary understanding.

Conclusions:

  • The developed method is the first to offer a standard of assessment for whole-genome phylogenetic analyses comparable to the classic bootstrap for aligned sequences.
  • The method's support values and receiver-operating characteristics are similar to the classic bootstrap, ensuring comparable sensitivity and specificity.
  • This assessment method enhances confidence in phylogenetic analyses of whole genomes, with potential extensions to search-based inference methods.