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,...
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 kingdom.
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...
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.

You might also read

Related Articles

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

Sort by
Same author

Population-scale Long-read Sequencing in the <i>All of Us</i> Research Program.

medRxiv : the preprint server for health sciences·2025
Same author

Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery.

bioRxiv : the preprint server for biology·2025
Same author

K-mer analysis of long-read alignment pileups for structural variant genotyping.

Nature communications·2025
Same author

K-mer analysis of long-read alignment pileups for structural variant genotyping.

bioRxiv : the preprint server for biology·2024
Same author

Cue: a deep-learning framework for structural variant discovery and genotyping.

Nature methods·2023
Same author

Fast and compact matching statistics analytics.

Bioinformatics (Oxford, England)·2022

Related Experiment Video

Updated: May 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

Phylogeny construction with rigid gapped motifs.

Fabio Cunial1, Alberto Apostolico

  • 1School of Computational Science and Engineering, College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA. fabio.cunial@gatech.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|June 27, 2012
PubMed
Summary

This study explores gapped motifs for phylogenetic reconstruction in mitochondrial proteomes. Gapped motifs, particularly longer, sparser ones with 3-4 solid characters, yield high-quality phylogenies comparable to existing alignment-free methods.

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Related Experiment Videos

Last Updated: May 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

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional phylogenetic methods often rely on ungapped sequence blocks.
  • Alignment-free algorithms typically compare ungapped blocks in genomes and proteomes.
  • Gapped motifs offer a potentially richer feature set for phylogenetic analysis.

Purpose of the Study:

  • To evaluate the effectiveness of gapped motifs in reconstructing phylogenies from mitochondrial proteomes.
  • To investigate the relationship between gapped motif characteristics (density, solid characters, significance) and phylogenetic quality.

Main Methods:

  • Reconstruction of phylogenies using sets of defined gapped motifs from mitochondrial proteomes.
  • Analysis of maximal motifs and their compact generators.
  • Assessment of motif properties including density, number of solid characters, and statistical significance.

Main Results:

  • The average performance of gapped motif sets is comparable to established string-based alignment-free methods.
  • Longer, sparser gapped motifs yield phylogenies of equal or superior quality compared to short, dense motifs.
  • Motifs with 3-4 solid characters produced the best phylogenies; increasing solid characters degraded performance.
  • Excluding motifs with low statistical significance reduced phylogenetic quality.
  • Higher redundancy in maximal motif bases improved phylogenetic reconstruction.

Conclusions:

  • Gapped motifs are a viable and effective tool for phylogenetic reconstruction in mitochondrial proteomes.
  • Specific characteristics of gapped motifs, such as length, sparsity, and number of solid characters, significantly influence phylogenetic accuracy.
  • Optimizing gapped motif selection criteria can enhance the performance of alignment-free phylogenetic methods.