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

5.8K
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...
5.8K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.1K
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...
7.1K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.0K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.0K
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

15.6K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
15.6K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

22
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...
22

You might also read

Related Articles

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

Sort by
Same author

Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.

Horticulture research·2026
Same author

OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.

Journal of molecular evolution·2025
Same author

Algorithms to reconstruct past indels: The deletion-only parsimony problem.

PLoS computational biology·2025
Same author

Link between the Birth-Death Process and the Kingman Coalescent-Applications to Phylogenetic Epidemiology.

Systematic biology·2025
Same author

Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation.

Analytical chemistry·2024
Same author

dipwmsearch: a Python package for searching di-PWM motifs.

Bioinformatics (Oxford, England)·2023

Related Experiment Video

Updated: Jul 11, 2025

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

993

EPIK: precise and scalable evolutionary placement with informative k-mers.

Nikolai Romashchenko1, Benjamin Linard1, Fabio Pardi1

  • 1LIRMM, University of Montpellier, CNRS, Montpellier, France.

Bioinformatics (Oxford, England)
|November 17, 2023
PubMed
Summary

Phylogenetic placement tools IPK and EPIK efficiently analyze large DNA datasets using filtered phylo-k-mers. These methods improve speed for massive sequence analysis while maintaining accurate phylogenetic placements.

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

2.2K
Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

7.6K

Related Experiment Videos

Last Updated: Jul 11, 2025

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

993
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

2.2K
Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

7.6K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Phylogenetics

Background:

  • Phylogenetic placement is crucial for analyzing large DNA collections when de novo tree inference is challenging.
  • Alignment-free methods, particularly those using phylo-k-mers, offer an alternative but face computational hurdles.
  • Reference data preprocessing and managing numerous k-mers limit current phylo-k-mer approaches.

Purpose of the Study:

  • To develop a more efficient method for phylogenetic placement using phylo-k-mers.
  • To introduce novel software tools that address the limitations of existing phylo-k-mer based approaches.
  • To enhance the speed and scalability of analyzing large-scale genomic datasets.

Main Methods:

  • A filtering method based on mutual information was developed to select informative phylo-k-mers.
  • The filtering method was implemented in IPK (Inference of Phylo-k-mers) for computing phylo-k-mers.
  • EPIK (Efficient Phylogenetic Inference using k-mers) was developed to support filtered phylo-k-mer databases for placement.

Main Results:

  • The proposed filtering method significantly improves placement efficiency with minimal accuracy loss.
  • IPK demonstrates superior performance in computing phylo-k-mers compared to existing software.
  • EPIK emerges as the fastest available tool for phylogenetic placement of millions of sequences, ensuring high accuracy.

Conclusions:

  • IPK and EPIK offer a substantial advancement in the efficiency and scalability of phylogenetic placement.
  • The developed filtering strategy effectively addresses computational bottlenecks in phylo-k-mer analysis.
  • These tools provide a powerful solution for large-scale phylogenetic analyses in bioinformatics.