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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.3K
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...
7.3K
Microbial Phylogeny01:28

Microbial Phylogeny

79
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,...
79
Genome Copying Errors02:46

Genome Copying Errors

5.7K
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
5.7K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

13.9K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
13.9K
Phylogeny01:23

Phylogeny

64.8K
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.
64.8K
Phylogenetic Trees03:21

Phylogenetic Trees

52.4K
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.
52.4K

You might also read

Related Articles

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

Sort by
Same author

Changes in Child Behaviour Following a Brief Parenting Intervention (Triple P) for Families of Children with Phenylketonuria (PKU): A Case Series.

Behavior modification·2026
Same author

Elephant range and population, strontium isotopes, and genetics combine to give local-scale specificity to ivory hotspot tracking.

Isotopes in environmental and health studies·2025
Same author

Enhancing Patient-Trial Matching With Large Language Models: A Scoping Review of Emerging Applications and Approaches.

JCO clinical cancer informatics·2025
Same author

Development of a Novel Ulcerative Colitis Endoscopic Mayo Score Prediction Model Using Machine Learning.

Gastro hep advances·2024
Same author

Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression.

Nature communications·2022
Same author

Elephant genotypes reveal the size and connectivity of transnational ivory traffickers.

Nature human behaviour·2022
Same journal

Duplication-based genetic dissection of the Down syndrome critical region reveals its complex functional organization.

G3 (Bethesda, Md.)·2026
Same journal

The complete sequence of the silkworm W chromosome uncovers its rapid evolution by large-scale duplications/deletions and translocation of W-linked genes.

G3 (Bethesda, Md.)·2026
Same journal

Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication.

G3 (Bethesda, Md.)·2026
Same journal

Deconstructing empirical fitness seascapes across scales of granularity.

G3 (Bethesda, Md.)·2026
Same journal

Genomes of Conopholis americana and Epifagus virginiana: Two holoparasitic plants (Orobanchaceae).

G3 (Bethesda, Md.)·2026
Same journal

"A chromosome-level reference genome for the colonial marine hydrozoan Podocoryna americana".

G3 (Bethesda, Md.)·2026
See all related articles

Related Experiment Video

Updated: Apr 21, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.7K

Correcting for sequencing error in maximum likelihood phylogeny inference.

Mary K Kuhner1, James McGill2

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065 mkkuhner@uw.com.

G3 (Bethesda, Md.)
|November 8, 2014
PubMed
Summary
This summary is machine-generated.

Correcting for DNA sequencing error improves phylogenetic accuracy, especially for branch lengths. Even approximate error rates enhance evolutionary studies, making this method preferable to ignoring potential errors.

Keywords:
maximum likelihoodphylogeny inferencesequencing error

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.7K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.3K

Related Experiment Videos

Last Updated: Apr 21, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.7K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.7K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.3K

Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Genomics

Background:

  • Accurate phylogenetic trees are essential for understanding evolutionary patterns and taxonomy.
  • Branch lengths in phylogenies are crucial for accurate dating and evolutionary rate estimations.
  • Unaccounted DNA sequencing error can compromise the reliability of phylogenetic analyses.

Purpose of the Study:

  • To evaluate the effectiveness of a DNA sequencing error correction method in maximum likelihood phylogeny inference.
  • To assess the impact of varying error rates and data polymorphism on phylogenetic accuracy.
  • To determine if correction with an approximate error rate is beneficial compared to ignoring sequencing errors.

Main Methods:

  • Utilized simulated DNA sequence data to test a specific correction method for sequencing errors.
  • Varied parameters including data polymorphism levels and true error rates in simulations.
  • Analyzed the recovery of both tree topology and branch lengths under different correction scenarios.

Main Results:

  • Correction for DNA sequencing error consistently improved the recovery of branch lengths across tested conditions.
  • The benefits to branch length accuracy persisted even when the assumed error rate was double the true rate.
  • While low error rates had minimal impact on topology, correction improved topological inference at higher error rates.
  • Extremely high error rates, when overestimated by the correction method, led to poor recovery of both topology and branch lengths.

Conclusions:

  • Correcting for DNA sequencing error is generally advantageous for improving phylogenetic accuracy, particularly for branch lengths.
  • Using an approximate error rate for correction is preferable to not addressing sequencing errors at all.
  • Despite its potential benefits, this error correction method has not been widely adopted, possibly due to reluctance in estimating error rates.