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Related Concept Videos

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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.
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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.
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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...
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A Practical Guide to Phylogenetics for Nonexperts
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tinselR-an R Shiny Application for Annotating Phylogenetic Trees.

Jennafer A P Hamlin1,2, Teofil Nakov3, Amanda Williams-Newkirk2

  • 1Association of Public Health Laboratories Bioinformatics, Silver Spring, Maryland, USA.

Microbiology Resource Announcements
|July 8, 2021
PubMed
Summary
This summary is machine-generated.

Public health labs use whole-genome sequencing for outbreak analysis. The new tinselR application simplifies pathogen relatedness visualization and annotation using phylogenetic trees.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Public Health

Background:

  • Public health laboratories rely on whole-genome sequencing for pathogen surveillance.
  • Identifying transmission routes and confirming outbreaks are critical public health functions.
  • Analyzing pathogen relatedness is a key step in outbreak investigations.

Purpose of the Study:

  • To introduce tinselR, a novel open-source application.
  • To provide a user-friendly tool for visualizing and annotating pathogen relatedness.
  • To streamline the analysis of pathogen whole-genome sequences.

Main Methods:

  • Development of an open-source application named tinselR.
  • Integration of visualization and annotation functionalities.
  • Application of phylogenetic tree analysis for pathogen relatedness.

Main Results:

  • tinselR offers a simplified approach to pathogen analysis.
  • The application facilitates the visualization of relatedness among pathogens.
  • Annotation features enhance the interpretation of phylogenetic data.

Conclusions:

  • tinselR effectively combines annotation and phylogenetics.
  • The tool simplifies a critical step in the pathogen analysis workflow.
  • This application supports public health laboratories in outbreak investigations.