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

6.2K
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...
6.2K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.3K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.3K
Phylogenetic Trees03:21

Phylogenetic Trees

46.5K
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.
46.5K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.4K
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...
7.4K
Phylogeny01:23

Phylogeny

47.3K
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.
47.3K
The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

The Tree of Life - Bacteria, Archaea, Eukaryotes

33.9K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
33.9K

You might also read

Related Articles

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

Sort by
Same author

A long non-coding RNA regulates in vitro and in vivo triazole antifungal susceptibility in Aspergillus fumigatus.

Genetics·2026
Same author

An epigenetic mechanism of azole tolerance facilitates acquired antifungal resistance in <i>Aspergillus fumigatus</i>.

mBio·2026
Same author

Novel Glomeromycotina-moss associations identified in California dryland biocrusts.

The New phytologist·2026
Same author

Genomic and Ecological Flexibility Shape the Global Distribution of a Black Fungus.

Environmental microbiology·2026
Same author

An epigenetic mechanism of azole tolerance facilitates acquired antifungal resistance in <i>Aspergillus fumigatus</i>.

bioRxiv : the preprint server for biology·2026
Same author

Thermal adaptation crosstalk with azole response through lncRNA in <i>Aspergillus fumigatus</i>.

bioRxiv : the preprint server for biology·2026
Same journal

A human-specific genetic modifier reconfigures large-scale cortical network dynamics underlying behavioral performance.

bioRxiv : the preprint server for biology·2026
Same journal

<i>Staphylococcus aureus</i> uses a eukaryotic-like uridyltransferase to make UDP-GlcNAc for cell wall synthesis.

bioRxiv : the preprint server for biology·2026
Same journal

Dynamic redistribution of eIF4F controls cap-dependent translation initiation.

bioRxiv : the preprint server for biology·2026
Same journal

When does additional information improve accuracy of RNA secondary structure prediction?

bioRxiv : the preprint server for biology·2026
Same journal

Normative brain-state trajectories reveal deviation from healthy aging in Alzheimer's disease.

bioRxiv : the preprint server for biology·2026
Same journal

Noradrenergic infraslow rhythm during sleep is the critical link between heart-rate dynamics and memory consolidation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Sep 12, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.0K

Phyling: phylogenetic inference from annotated genomes.

Cheng-Hung Tsai1,2, Jason Eric Stajich1,3

  • 1Department of Microbiology & Plant Pathology, University of California-Riverside, Riverside, CA 92521, United States.

Biorxiv : the Preprint Server for Biology
|August 6, 2025
PubMed
Summary
This summary is machine-generated.

Phyling is a new tool for building species phylogenies from genomic data. It is faster and as accurate as other methods, offering a user-friendly experience for large-scale phylogenomic reconstruction.

Keywords:
Hidden Markov ModelsPythonorthologyphylogeneticsphylogenomicssoftware

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

2.3K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.5K

Related Experiment Videos

Last Updated: Sep 12, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.0K
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

2.3K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenetic reconstruction is crucial for understanding evolutionary relationships.
  • Existing methods can be computationally intensive and slow for large datasets.

Purpose of the Study:

  • To introduce Phyling, a novel tool for rapid and scalable phylogenomic reconstruction.
  • To provide a user-friendly solution for species phylogeny inference directly from genomic data.

Main Methods:

  • Phyling identifies orthologous genes using Hidden Markov Models (HMMs) from the BUSCO database.
  • It supports both consensus and concatenation strategies for species tree construction.
  • The tool optimizes memory usage and data processing for efficiency.

Main Results:

  • Phyling demonstrates significantly faster performance compared to OrthoFinder.
  • It achieves equal or superior accuracy in phylogenetic reconstruction.
  • The checkpoint system allows for incremental analysis, saving computational resources.

Conclusions:

  • Phyling offers an efficient, accurate, and scalable solution for phylogenomic reconstruction.
  • Its user-friendly design and features like checkpointing make it suitable for large-scale evolutionary studies.
  • The tool supports both protein and nucleotide data for versatile phylogenetic analyses.