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.
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.
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...
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

Machine learning-driven correction of handgrip strength: a novel biomarker for neurological and health outcomes in the UK Biobank.

Biomedical physics & engineering express·2026
Same author

Biological brain aging, cognitive-motor decline and vascular risk: a multivariate imaging analysis of 40,579 individuals.

Frontiers in aging neuroscience·2026
Same author

Linking human brain functional connectivity to underlying neurotransmission.

bioRxiv : the preprint server for biology·2026
Same author

Predicting brain volumes from anthropometric and demographic features: insights from UK biobank neuroimaging data.

Brain structure & function·2026
Same author

Longitudinal brain-age predictions comprising long-duration spaceflight missions.

NPJ microgravity·2026
Same author

Can we predict sleep health based on brain features? A large-scale machine learning study using the UK Biobank.

Brain communications·2026

Related Experiment Video

Updated: May 9, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Alignment-free genome tree inference by learning group-specific distance metrics.

Kaustubh R Patil1, Alice C McHardy

  • 1Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany. patil@mpi-inf.mpg.de

Genome Biology and Evolution
|July 12, 2013
PubMed
Summary

This study introduces a novel alignment-free method using genome signatures to infer evolutionary relationships. It enhances taxonomic distance accuracy by learning group-specific metrics for improved genome tree inference.

Keywords:
alignmentalignment-freedistance metric learninggenome signaturegenome treesequence comparisontaxonomy

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

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: May 9, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

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:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Inferring evolutionary relationships is crucial for organismal study.
  • Traditional gene-based methods have limitations.
  • Genome-scale data offers new opportunities but poses computational challenges.

Purpose of the Study:

  • To develop a computationally efficient method for inferring taxonomic distances using genome-scale information.
  • To improve genome tree inference by learning specialized distance metrics.
  • To compare the performance of alignment-free and alignment-based methods.

Main Methods:

  • Utilized genome signatures for alignment-free sequence comparison.
  • Developed a method to learn group-specific Mahalanobis distance metrics guided by a reference taxonomy.
  • Applied the method to over a thousand prokaryotic genomes and compared 10 different inference methods.

Main Results:

  • Demonstrated improved distance metrics for most tested organism groups.
  • Showcased the effectiveness of learned group-specific metrics for enhancing genome tree accuracy.
  • Provided a large-scale comparison of nine alignment-free and one alignment-based method.

Conclusions:

  • Learned group-specific distance metrics significantly improve taxonomic distance estimation.
  • The proposed alignment-free approach offers a computationally efficient and accurate method for phylogenetic inference.
  • This method facilitates more precise evolutionary relationship studies across diverse prokaryotic groups.