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

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...
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,...
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...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

You might also read

Related Articles

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

Sort by
Same author

Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.

Nutrients·2026
Same author

Min-frame transformation enables more sensitive viral genome alignment.

bioRxiv : the preprint server for biology·2026
Same author

TIPP-SD: A new method for species detection in microbiomes.

PLoS computational biology·2026
Same author

Minimally-invasive resection of deep-seated subcortical and intraventricular lesions using an integrated camera-port system: A retrospective case series.

PloS one·2026
Same author

Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

FLASH Radiotherapy Mitigates Radiation-Induced Lymphopenia and Prevents Immunosuppression via Chk1-STAT3 Axis Modulation in a Preclinical Thoracic Irradiation Model.

International journal of radiation oncology, biology, physics·2026
Same journal

Measuring Mosquito-borne Viral Suitability in Myanmar and Implications for Local Zika Virus Transmission.

PLoS currents·2019
Same journal

Drought in the Semiarid Region of Brazil: Exposure, Vulnerabilities and Health Impacts from the Perspectives of Local Actors.

PLoS currents·2018
Same journal

Estimation of Pneumonic Plague Transmission in Madagascar, August-November 2017.

PLoS currents·2018
Same journal

Does the Humanitarian Sector Use Evidence-informed Standards? A Review of the 2011 Sphere Indicators for Wash, Food Security and Nutrition, and Health Action.

PLoS currents·2018
Same journal

Uganda at Glance of 5.7 Magnitude Earthquake: Lessons for Earthquake Risk Reduction.

PLoS currents·2018
Same journal

Neurodevelopmental Needs in Young Boys with Duchenne Muscular Dystrophy (DMD): Observations from the Cooperative International Neuromuscular Research Group (CINRG) DMD Natural History Study (DNHS).

PLoS currents·2018
See all related articles

Related Experiment Video

Updated: Jun 6, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and

C Randal Linder1, Rahul Suri, Kevin Liu

  • 1Integrative Biology, University of Texas; University of Texas; The University of Texas and Microsoft Research New England, and The Department of Computer Science, University of Texas at Austin.

Plos Currents
|November 30, 2010
PubMed
Summary
This summary is machine-generated.

Researchers created benchmark datasets and tools to evaluate computational methods for evolutionary relationship estimation. This resource aids in developing new alignment and tree inference methods for complex biological data.

More Related Videos

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Related Experiment Videos

Last Updated: Jun 6, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Accurate estimation of evolutionary relationships is crucial in biology.
  • Existing computational methods face challenges with complex datasets, including multiple sequence alignment and phylogeny estimation.
  • There is a need for standardized benchmarks to evaluate and improve these methods.

Purpose of the Study:

  • To provide a comprehensive collection of benchmark datasets and software tools.
  • To facilitate the evaluation of accuracy and scalability of computational methods for evolutionary relationship estimation.
  • To support the development of novel alignment and tree inference methods.

Main Methods:

  • Assembly of web pages containing benchmark datasets and software tools.
  • Inclusion of empirical datasets with curated alignments for testing alignment and phylogenetic methods.
  • Provision of simulated datasets mimicking large-scale systematics studies, with true alignments and trees.
  • Inclusion of links to external empirical datasets and software for data generation and evaluation.

Main Results:

  • A curated collection of benchmark datasets for multiple sequence alignment, phylogeny estimation, and supertree estimation.
  • Availability of simulated datasets with challenging properties like high substitution and indel rates.
  • Links to relevant software tools for data simulation and method evaluation.
  • A resource designed to address the needs of large-scale systematics studies.

Conclusions:

  • The developed resource provides a valuable platform for the scientific community to test and enhance computational methods in evolutionary biology.
  • It specifically aids in addressing challenges related to multiple sequence alignment and phylogeny estimation on difficult datasets.
  • The benchmark datasets and tools are intended to drive innovation in the development of more accurate and scalable bioinformatics tools.