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

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,...

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...

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...

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

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

Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.

bioRxiv : the preprint server for biology·2026

Same author

Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.

Methods in molecular biology (Clifton, N.J.)·2026

Same author

Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.

bioRxiv : the preprint server for biology·2026

Same author

A large language model-based tool for identifying relationships to industry in research on the carcinogenicity of benzene, cobalt, and aspartame.

Environmental health : a global access science source·2025

Same author

A survey of computational approaches for characterizing microbial interactions in microbial mats.

Genome biology·2025

Same author

Polyphest: fast polyploid phylogeny estimation.

Bioinformatics (Oxford, England)·2024

Search research articles

Related Experiment Video

Updated: Jul 3, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.

Cuong Than¹, Derek Ruths, Luay Nakhleh

¹Department of Computer Science, Rice University, 6100 Main Street, MS 132, Houston, TX, USA. cvthan@cs.rice.edu

BMC Bioinformatics

|July 30, 2008

Summary

This summary is machine-generated.

PhyloNet is a new software package for analyzing evolutionary networks, which represent complex reticulate evolutionary events like horizontal gene transfer. It offers tools for network representation, characterization, comparison, and reconstruction, improving the analysis of complex biological histories.

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: Jul 3, 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
Bioinformatics
Evolutionary Biology

Background:

Phylogenetic analyses traditionally assume tree-like evolutionary histories.
Complex evolutionary events, such as horizontal gene transfer (HGT), hybrid speciation, and recombination, result in reticulate evolutionary networks, not trees.
Existing software tools for reticulate evolution analysis include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.

Purpose of the Study:

To introduce PhyloNet, a software package designed for the analysis of reticulate evolutionary relationships and evolutionary networks.
To provide a suite of tools for various aspects of evolutionary network analysis.

Main Methods:

PhyloNet categorizes its tools into four main areas: representation, characterization, comparison, and reconstruction of evolutionary networks.
Evolutionary networks are represented as rooted, directed, acyclic graphs, leaf-labeled by taxa.
The software supports a new compact format (eNewick) for evolutionary network representation.

Main Results:

PhyloNet offers utilities for reading/writing evolutionary networks in a compact form.
It enables the analysis of evolutionary networks based on trees, clusters, and tripartitions.
The package facilitates comparison of evolutionary networks based on topological dissimilarities and sequence evolution fitness.
PhyloNet can reconstruct evolutionary networks from species and gene trees.

Conclusions:

PhyloNet provides efficient and accurate tools for analyzing evolutionary networks.
The software aids in analyzing large datasets and evaluating evolutionary network reconstruction methods.
Support for the eNewick format enhances interoperability between different evolutionary network software tools.