Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Phylogeny

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.

Evolutionary Relationships through Genome Comparisons

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 Phylogeny

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 Trees

Phylogenetic Trees

Phylogenetic Trees

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.

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

You might also read

Related Articles

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

Sort by

Same author

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics.

bioRxiv : the preprint server for biology·2026

Same author

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026

Same author

piqtree: a python package for seamless phylogenetic inference with IQ-TREE.

Molecular biology and evolution·2026

Same author

How Does Transcription-Associated Mutagenesis Shape tRNA Microevolution?

Genome biology and evolution·2026

Same author

Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.

Genome biology and evolution·2026

Same author

Comparing partition and mixture models with akaike information criteria.

Systematic biology·2026

Same journal

Phylogenomic blind spots: The limits of UCE and BUSCO loci in the presence of gene flow.

Molecular biology and evolution·2026

Same journal

seqLens: optimizing language models for genomic predictions.

Molecular biology and evolution·2026

Same journal

The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.

Molecular biology and evolution·2026

Same journal

800 million years of co-evolution in the green plant lineage - the case of LEUNIG and SEUSS transcriptional co-regulators.

Molecular biology and evolution·2026

Same journal

RNA i-motif landscapes in plant kingdom and their potential functional roles.

Molecular biology and evolution·2026

Same journal

Functional Divergence and Structural Changes of class IV Histone Deacetylases (HDACs) Across the Tree of Life.

Molecular biology and evolution·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 7, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

IQ-TREE 3: phylogenomic inference software using complex evolutionary models.

Thomas K F Wong^1,2, Nhan Ly-Trong¹, Huaiyan Ren¹

¹School of Computing, College of Systems and Society, Australian National University, Canberra, ACT, Australia.

Molecular Biology and Evolution

|May 5, 2026

Summary

This summary is machine-generated.

IQ-TREE version 3 is a new release of phylogenetic tree inference software. This update introduces mixture models, concordance factors for genomic discordance, and divergence time estimation integration.

Keywords:

concordance factor maximum likelihood mixture model phylogenetic software phylogenomic software sequence simulator

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

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 7, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

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

Published on: July 11, 2025

Area of Science:

Computational Biology
Phylogenetics
Bioinformatics

Background:

IQ-TREE is a popular open-source tool for phylogenetic tree inference using maximum likelihood.
The previous version, IQ-TREE 2, established a robust foundation for evolutionary analyses.

Purpose of the Study:

To introduce IQ-TREE version 3, the latest major release of the phylogenetic inference software.
To highlight significant new features and improvements over IQ-TREE version 2.

Main Methods:

Development and implementation of new algorithms within the IQ-TREE software framework.
Integration of novel statistical methods for phylogenetic analysis.

Main Results:

IQ-TREE 3 incorporates mixture models as an alternative to partitioned models.
New features include gene and site concordance factors to assess genomic region discordance.
Integration with phylogenomic divergence time estimation and a sequence simulator are now available.

Conclusions:

IQ-TREE 3 offers enhanced capabilities for phylogenetic tree inference and evolutionary analysis.
The new features provide more accurate and comprehensive insights into evolutionary relationships and genomic discordance.