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,...
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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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...
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...

You might also read

Related Articles

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

Sort by
Same author

Epistasis plays a limited role in driving entrenchment during neutral protein evolution.

Genome biology·2026
Same author

Empowering Inference of Epistasis on the Basis of Mutual Exclusivity, Co-Occurrence, Functional Antagonism and Synergy in ERK-Pathway Oncogenes.

International journal of cancer·2026
Same author

Accelerating discovery of cancer causes for prevention in the era of rising early-onset cancers.

Cell·2026
Same author

Cost-Effectiveness of Perioperative Durvalumab With Neoadjuvant Gemcitabine/Cisplatin in Muscle-Invasive Bladder Cancer Treatment.

Journal of the National Comprehensive Cancer Network : JNCCN·2026
Same author

DMEM and EMEM as alternate growth media for pathogenic Leptospira.

PLoS neglected tropical diseases·2026
Same author

Competing subclones and fitness diversity shape tumor evolution across cancer types.

Bioinformatics (Oxford, England)·2026

Related Experiment Video

Updated: Jun 1, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyDesign: an online application for profiling phylogenetic informativeness.

Francesc López-Giráldez1, Jeffrey P Townsend

  • 1Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA. francesc.lopez@gmail.com

BMC Evolutionary Biology
|June 2, 2011
PubMed
Summary
This summary is machine-generated.

PhyDesign is a new online tool that helps scientists choose the best genes for phylogenetic studies. It prioritizes genetic markers, improving the efficiency and accuracy of evolutionary research.

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

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

Related Experiment Videos

Last Updated: Jun 1, 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

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

Area of Science:

  • Evolutionary Biology
  • Bioinformatics

Background:

  • Increasing genomic data necessitates efficient methods for phylogenetic marker selection.
  • Existing methods lack user-friendly tools for locus prioritization based on phylogenetic informativeness.

Purpose of the Study:

  • To introduce PhyDesign, an online application for evaluating phylogenetic informativeness.
  • To provide a quantitative method for selecting optimal genetic markers for phylogenetic analyses.

Main Methods:

  • Implementation of the Townsend (2007) phylogenetic informativeness metric.
  • Development of a platform-independent online application with an intuitive interface.
  • Calculation and visualization of informativeness profiles over specified time ranges.

Main Results:

  • PhyDesign quantitatively predicts the utility of genetic loci for phylogenetic questions.
  • The application ranks loci for prioritization across different evolutionary epochs.
  • User-friendly interface allows uploading of sequence alignments and ultrametric trees.

Conclusions:

  • PhyDesign enhances the efficiency and accuracy of phylogenetic studies.
  • Facilitates cost-effective locus selection compared to traditional screening methods.
  • Freely accessible online tool with supporting documentation.