Related Experiment Video
Updated: Mar 25, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
16.6K
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
Jaime Huerta-Cepas1, François Serra2, Peer Bork3
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany huerta@embl.de.
Molecular Biology and Evolution
|February 28, 2016
Summary
The Environment for Tree Exploration (ETE) v3 is a powerful computational framework for phylogenetic tree analysis. It offers new tools for building phylogenies, testing evolutionary models, and integrating with the NCBI taxonomy database.
Area of Science:
- Computational Biology
- Phylogenetics
- Genomics
Background:
- Phylogenetic tree reconstruction and analysis are crucial in evolutionary biology.
- Existing computational frameworks can be complex and lack integrated functionalities.
- The Environment for Tree Exploration (ETE) provides a unified platform for these tasks.
Purpose of the Study:
- To introduce ETE v3, an updated version of the computational framework.
- To present novel standalone tools and significant improvements for phylogenetic analysis.
- To enhance usability and integration with external biological databases.
Main Methods:
- Development of a new library of methods for phylogenetic analysis.
- Implementation of standalone tools for common comparative genomics and phylogenetics tasks.
- Integration with the NCBI taxonomy database for enhanced data retrieval.
Main Results:
- ETE v3 enables single-command construction of gene-based and supermatrix-based phylogenies.
- The framework facilitates testing and visualization of evolutionary models.
- New functionalities allow distance calculations between trees of varying sizes and complexities, including duplications.
- Seamless integration with the NCBI taxonomy database is now provided.
Conclusions:
- ETE v3 offers a comprehensive and user-friendly solution for phylogenetic analysis.
- The enhanced features streamline common tasks in comparative genomics and phylogenetics.
- The framework is freely available, promoting wider adoption in the scientific community.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
7.2K
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...
7.2K
01:28Microbial Phylogeny
22
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,...
22
01:23Phylogeny
64.4K
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.
64.4K
03:21Phylogenetic Trees
51.7K
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.
51.7K
03:21Phylogenetic Trees
6.8K
6.8K
01:20Applications of Molecular Taxonomy
653
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...
653