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Related Concept Videos

Phylogenetic Trees03:21

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 Trees03:21

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

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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 extant and...
The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

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Collecting and Processing Drone-based Remotely Sensed Data for Use in Forest Recovery Monitoring
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ETE: a python Environment for Tree Exploration.

Jaime Huerta-Cepas1, Joaquín Dopazo, Toni Gabaldón

  • 1Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain. jhuerta@crg.es

BMC Bioinformatics
|January 15, 2010
PubMed
Summary
This summary is machine-generated.

The Environment for Tree Exploration (ETE) is a Python toolkit for automated analysis and visualization of hierarchical trees. It offers scalable solutions for large-scale bioinformatics surveys, enhancing tree data manipulation and interpretation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Hierarchical trees are crucial outputs in bioinformatics analyses like phylogenetics and gene clustering.
  • Existing tools often lack scalability and automation for large-scale genome-wide surveys.
  • There's a growing demand for efficient tools to manage and analyze large tree structures.

Purpose of the Study:

  • To introduce the Environment for Tree Exploration (ETE) toolkit.
  • To provide automated manipulation, analysis, and visualization of hierarchical trees.
  • To address the need for scalable tree handling in large-scale bioinformatics.

Main Methods:

  • Developed a Python programming toolkit (ETE).
  • Implemented libraries for tree manipulation, analysis, and visualization.
  • Integrated features for independent partition analysis, extended Newick format support, node annotation, and linking to external data.

Main Results:

  • ETE facilitates automated analysis and visualization of hierarchical trees.
  • The toolkit supports phylogenetic and clustering trees with advanced features.
  • Includes built-in tools for orthology prediction and cluster validation.
  • Offers a programmable engine for customized tree rendering.

Conclusions:

  • ETE provides comprehensive methods for tree data structure manipulation, extending existing bioinformatics toolkits.
  • The toolkit offers enhanced functionality for analyzing and visualizing large-scale tree data.
  • ETE is freely available, promoting wider adoption in bioinformatics research.