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

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...
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...
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...
Parseval's Theorem for Fourier transform01:15

Parseval's Theorem for Fourier transform

Parseval's theorem is a fundamental principle in signal processing that enables the calculation of a signal's energy in either the time domain or the frequency domain. This theorem is pivotal in demonstrating energy conservation between these two domains, ensuring that the computed energy value remains consistent regardless of the domain of analysis.
To understand Parseval's theorem, it is essential to first comprehend how signal energy is typically calculated. When considering a signal's...

You might also read

Related Articles

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

Sort by
Same author

Artificial intelligence and machine learning: an important new set of tools for clinical shoulder arthroplasty research.

JSES international·2026
Same author

Replaying germinal center evolution on a quantified affinity landscape.

Cell·2026
Same author

Generalizing Matrix Representations to Fully Heterochronous Ranked Tree Shapes.

Bulletin of mathematical biology·2026
Same author

Entrenchment of germline amino-acid differences in antibody affinity maturation.

bioRxiv : the preprint server for biology·2026
Same author

Inference of germinal center evolutionary dynamics via simulation-based deep learning.

eLife·2026
Same author

Surgeon variation in the use of pre-operative imaging, 3D-based planning, and enabling technologies in shoulder arthroplasty.

Journal of shoulder and elbow arthroplasty·2026

Related Experiment Video

Updated: Jun 26, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Fourier transform inequalities for phylogenetic trees.

Frederick A Matsen1

  • 1Department of Statistics, University of California, Berkeley, 367 Evans Hall #429, Berkeley, CA 94720-3860, USA. matsen@berkeley.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|January 31, 2009
PubMed
Summary

New "edge-parameter inequalities" constrain phylogenetic site-pattern frequencies beyond invariants. These mathematical constraints ensure accurate phylogenetic tree reconstruction by defining valid frequency vectors for evolutionary models.

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

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

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

Published on: October 16, 2018

Related Experiment Videos

Last Updated: Jun 26, 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

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

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

Published on: October 16, 2018

Area of Science:

  • Computational Biology
  • Phylogenetics
  • Mathematical Biology

Background:

  • Phylogenetic invariants are known constraints on site-pattern frequency vectors.
  • Existing constraints do not fully capture all valid frequency vectors for phylogenetic trees.

Purpose of the Study:

  • To introduce and define novel constraints, termed "edge-parameter inequalities," for phylogenetic site-pattern frequency vectors.
  • To demonstrate the inadequacy of current constraints using a pathological quartet tree example.
  • To provide a complete set of inequalities for group-based models.

Main Methods:

  • Derivation of edge-parameter inequalities based on the properties of mutation matrices.
  • Analysis of a pathological site-pattern frequency vector violating existing literature constraints.
  • Formulation of two complete sets of inequalities in Fourier transformed coordinates for group-based models.

Main Results:

  • Identified a pathological site-pattern frequency vector that satisfies existing phylogenetic constraints but represents an invalid tree.
  • Developed two finite lists of "monomial <= 1" inequalities in Fourier coordinates.
  • These inequalities, combined with phylogenetic invariants, fully characterize valid site-pattern frequency vectors for phylogenetic trees.

Conclusions:

  • Edge-parameter inequalities are crucial for fully defining the space of valid phylogenetic site-pattern frequency vectors.
  • The presented inequalities provide a complete mathematical description of phylogenetically relevant semialgebraic subsets.
  • This work enhances the mathematical framework for phylogenetic tree inference.