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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...
Phylogeny01:23

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...
Evolutionary Relationships through Genome Comparisons02:54

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 Phylogeny01:28

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

The Tree of Life - Bacteria, Archaea, Eukaryotes

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...

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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

TreeVector: scalable, interactive, phylogenetic trees for the web.

Ralph Pethica1, Gary Barker, Tim Kovacs

  • 1Computer Science Department, University of Bristol, Bristol, United Kingdom. pethica@cs.bris.ac.uk

Plos One
|February 4, 2010
PubMed
Summary
This summary is machine-generated.

TreeVector offers a new method for visualizing complex phylogenetic trees interactively in web browsers. This approach enhances data exploration for large-scale biological analyses, moving beyond static images.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Phylogenetic trees are complex data structures requiring graphical representation for human comprehension.
  • Traditional static image rendering of phylogenetic trees is insufficient for the growing volume of biological data and large-scale analyses.
  • There is a need for scalable, browsable, and interactive tree visualizations.

Purpose of the Study:

  • To introduce TreeVector, a novel method for interactive phylogenetic tree visualization.
  • To enable seamless integration and viewing of phylogenetic trees in standard web browsers.
  • To facilitate modification and linking of trees using standard web technologies.

Main Methods:

  • Developed TreeVector using Scalable Vector Graphics (SVG) and Java.
  • Designed TreeVector as a framework for integration with bioinformatics servers and databases.
  • Enabled automatic production of user-customized phylogenies.

Main Results:

  • TreeVector allows phylogenetic trees to be viewed and interacted with in standard web browsers without requiring additional software.
  • The method supports modification and linking of trees via standard web technologies.
  • TreeVector is designed to integrate with dynamic bioinformatics processes and databases.

Conclusions:

  • TreeVector is a fast, user-friendly, and open-source tool for phylogenetic tree visualization.
  • The software is available for download and can be run from a web server or a user's own server.
  • TreeVector has been successfully deployed on two prominent biological database websites.