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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.

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.

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

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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.

Modern Molecular Taxonomy

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...

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Related Experiment Video

Updated: May 24, 2026

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

A format for phylogenetic placements.

Frederick A Matsen¹, Noah G Hoffman, Aaron Gallagher

¹Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America. matsen@fhcrc.org

|March 3, 2012

Summary

We created a unified JSON format for phylogenetic placements, mapping environmental DNA sequences to phylogenetic trees. This standard enables efficient development of analysis tools for diverse applications.

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Last Updated: May 24, 2026

The ITS2 Database

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Published on: March 12, 2012

A Practical Guide to Phylogenetics for Nonexperts

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Bioinformatics
Computational Biology
Phylogenetics

Background:

Phylogenetic placement tools are rapidly advancing.
A lack of standardized formats hinders data sharing and tool development.
Environmental sequence data requires efficient mapping to phylogenetic trees.

Purpose of the Study:

To develop a unified, lightweight, and extensible format for phylogenetic placements.
To establish a standard for storing and analyzing mappings of environmental sequence data to phylogenetic trees.
To facilitate the development of portable post-analysis tools.

Main Methods:

Developed a JSON-based format for phylogenetic placements.
Ensured the format is versatile and extensible.
Implemented the format in parsimony- and likelihood-based placement tools.

Main Results:

A practical, unified format for phylogenetic placements has been established.
The format is compatible with existing programming languages and tools.
The format has been successfully used in practice for analyzing read placements.

Conclusions:

A standardized format is crucial for advancing phylogenetic placement analysis.
This new format promotes efficient development of post-analysis tools.
Widespread adoption will accelerate research in diverse applications of phylogenetic placement.