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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...
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...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

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...
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,...

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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

ColorTree: a batch customization tool for phylogenic trees.

Wei-Hua Chen1, Martin J Lercher

  • 1Bioinformatics, Heinrich-Heine University Duesseldorf, 40225, Germany. chen@cs.uni-duesseldorf.de

BMC Research Notes
|August 4, 2009
PubMed
Summary
This summary is machine-generated.

ColorTree is a batch customization tool that automates the coloring of phylogenetic trees. This software facilitates the visual inspection of large gene sets, improving evolutionary history analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Comparative genomics and genome sequencing generate large datasets of phylogenetic trees.
  • Manual inspection of numerous trees for evolutionary history analysis is time-consuming.
  • Visual aids like coloring schemes significantly aid in checking tree compatibility with null hypotheses.

Purpose of the Study:

  • Introduce ColorTree, a tool for automated batch customization of phylogenetic trees.
  • Enable efficient visual inspection of large sets of evolutionary trees.

Main Methods:

  • ColorTree utilizes pattern matching rules to customize tree files.
  • Customizations include coloring labels and branches.
  • The tool operates as a stand-alone command-line application on any Perl installation.

Main Results:

  • ColorTree applies user-defined rules to customize multiple tree files.
  • Customized trees are saved to output files for viewing in Dendroscope.
  • Automated customization allows processing hundreds of trees in minutes.

Conclusions:

  • ColorTree provides efficient and flexible visual customization for large phylogenetic tree sets.
  • The tool simplifies the analysis of evolutionary relationships by automating tree visualization.