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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...
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,...
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...
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...
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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Updated: Jun 23, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyloExplorer: a web server to validate, explore and query phylogenetic trees.

Vincent Ranwez1, Nicolas Clairon, Frédéric Delsuc

  • 1Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E, Bataillon - 34095 Montpellier Cedex 05, France. vincent.ranwez@univ-montp2.fr

BMC Evolutionary Biology
|May 20, 2009
PubMed
Summary
This summary is machine-generated.

PhyloExplorer is a new tool that helps manage collections of phylogenetic trees. It standardizes taxon names, selects relevant trees using queries, and finds complementary trees in databases.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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The ITS2 Database
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The ITS2 Database

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Last Updated: Jun 23, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Computational phylogenetics

Background:

  • Reconstructing molecular phylogenies is crucial for evolutionary biology.
  • Phylogenetic trees require manipulation for publications and analyses like supertree inference.
  • Existing tools lack comprehensive management for tree collections, including name standardization and subset selection.

Purpose of the Study:

  • To introduce PhyloExplorer, a tool for assessing and managing phylogenetic tree collections.
  • To address the limitations of current methods in handling multiple phylogenetic trees.
  • To facilitate the integration and analysis of diverse phylogenetic datasets.

Main Methods:

  • PhyloExplorer processes collections of rooted trees.
  • It offers functionalities for descriptive statistics and taxon name correction.
  • A dedicated query language enables extraction of taxonomically relevant subsets.
  • Integration with TreeBASE allows identification of related trees.

Main Results:

  • PhyloExplorer provides statistics for collection assessment.
  • It standardizes taxon names against a reference taxonomy.
  • Users can query and extract specific subsets of trees.
  • The tool identifies relevant and complementary trees from TreeBASE.

Conclusions:

  • PhyloExplorer is a user-friendly website utilizing Python and MySQL.
  • It simplifies the management and analysis of phylogenetic tree collections.
  • The tool enhances discoverability of relevant phylogenetic data.