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.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...
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...
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

High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.

Nucleic acids research·2026
Same author

HMMER web server: 2026 update.

Nucleic acids research·2026
Same author

What does it take to learn the rules of RNA base pairing? A lot less than you may think.

Communications biology·2026
Same author

Induction of menstruation in mice reveals the regulation of menstrual shedding.

bioRxiv : the preprint server for biology·2025
Same author

High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.

bioRxiv : the preprint server for biology·2025
Same author

All-at-once RNA folding with 3D motif prediction framed by evolutionary information.

Nature methods·2025

Related Experiment Video

Updated: Jul 1, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Probabilistic phylogenetic inference with insertions and deletions.

Elena Rivas1, Sean R Eddy

  • 1Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America. rivase@janelia.hhmi.org

Plos Computational Biology
|September 13, 2008
PubMed
Summary

This study introduces a new evolutionary model for sequence analysis that includes insertions and deletions alongside substitutions. This enhanced phylogenetic model improves accuracy in reconstructing evolutionary relationships, especially for ribosomal RNA alignments.

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

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Related Experiment Videos

Last Updated: Jul 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

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic models traditionally focus on substitution events, neglecting insertions and deletions.
  • Accurate evolutionary models are crucial for understanding sequence relationships and history.

Purpose of the Study:

  • To develop a probabilistic model for multiple sequence alignments that incorporates insertion and deletion events.
  • To improve phylogenetic tree inference by accounting for all major evolutionary events.

Main Methods:

  • Developed a generative evolutionary model using a continuous Markov process and a birth-death process for insertions/deletions.
  • Augmented the rate matrix with a gap character to model these events.
  • Extended the dnaml program (from phylip) to dnamlepsilon to implement the new model for phylogenetic tree inference.

Main Results:

  • The extended program dnamlepsilon demonstrates improved accuracy in phylogenetic tree inference compared to models ignoring gaps.
  • Benchmarking on simulated data and real ribosomal RNA alignments validated the model's effectiveness.
  • The new model retains the computational efficiency of the Felsenstein peeling algorithm.

Conclusions:

  • Accounting for insertion and deletion events significantly enhances the accuracy of phylogenetic analysis.
  • The developed model provides a more comprehensive approach to sequence evolution, applicable to various biological datasets.
  • dnamlepsilon offers a computationally efficient and accurate tool for phylogenetic inference in bioinformatics.