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Related Concept Videos

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,...
Phylogenetic Trees03:21

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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.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

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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.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

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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...
The Tree of Life - Bacteria, Archaea, 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...

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Updated: Jun 13, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Bayesian credible sets for phylogenetic tree topologies with applications to coverage analysis and cross-model

Jonathan Klawitter1, Alexei J Drummond2

  • 1School of Computer Science, University of Auckland, Auckland, Aotearoa New Zealand.

Molecular Biology and Evolution
|June 11, 2026
PubMed
Summary
This summary is machine-generated.

Bayesian phylogenetics now has new methods to define credible sets for tree topologies, addressing challenges with complex tree spaces. These novel approaches improve phylogenetic analysis and development using Conditional Clade Distributions (CCD).

Keywords:
Bayesian phylogeneticsconditional clade distributionscoverage analysiscredible set

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Last Updated: Jun 13, 2026

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Statistical Modeling

Background:

  • Credible intervals and sets are crucial in Bayesian phylogenetics for continuous parameters.
  • Defining credible sets for complex tree topologies is challenging due to unique sampled trees and diffuse posteriors.
  • Traditional frequency-based methods are insufficient for evaluating tree topology credibility.

Purpose of the Study:

  • To introduce novel and efficient methods for estimating the credible level of individual tree topologies.
  • To propose and define the concept of α credible Conditional Clade Distribution (CCD).
  • To develop algorithms for computing credible CCDs and determining credible levels for topologies and subtrees.

Main Methods:

  • Utilized tractable tree distributions, specifically Conditional Clade Distribution (CCD), for estimating topology credibility.
  • Developed algorithms for efficient computation of α credible CCDs.
  • Applied methods to simulated and real datasets for accuracy evaluation and performance assessment of CCD models.

Main Results:

  • Introduced novel methods for estimating credible levels of tree topologies using CCD.
  • Proposed the α credible CCD concept to quantify probability mass within a set of trees.
  • Demonstrated the utility of methods for rank-uniformity validation and Empirical Cumulative Distribution Function (ECDF) plots.

Conclusions:

  • The novel methods provide efficient and accurate ways to define credible sets for tree topologies in Bayesian phylogenetics.
  • The α credible CCD concept and associated algorithms enhance the analysis of complex phylogenetic posteriors.
  • These methods supplement standard analyses and offer new tools for validating phylogenetic models and results.