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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,...
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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...
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Phylogenetic Trees03:21

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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 kingdom.

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Updated: May 18, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Phylogenetics, likelihood, evolution and complexity.

A P Jason de Koning1, Wanjun Gu, Todd A Castoe

  • 1Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045, USA.

Bioinformatics (Oxford, England)
|September 15, 2012
PubMed
Summary
This summary is machine-generated.

Phylogenetics, Likelihood, Evolution and Complexity (PLEX) software accelerates large-scale phylogenetic analyses using novel methods. This Bayesian tool significantly reduces computation time for complex evolutionary models, making large datasets tractable.

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Last Updated: May 18, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

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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

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic analysis is crucial for understanding evolutionary relationships.
  • Analyzing large biological datasets with complex evolutionary models is computationally intensive.

Purpose of the Study:

  • To introduce Phylogenetics, Likelihood, Evolution and Complexity (PLEX), a novel software for phylogenetic analysis.
  • To present a fast and flexible Bayesian Markov chain Monte Carlo program for large-scale nucleotide and amino acid data analysis.

Main Methods:

  • Implementation of 'partial sampling of substitution histories' for data augmentation.
  • Utilizes efficient algorithms that scale with data size and model complexity.
  • Supports a variety of nucleotide and amino acid substitution models, including non-reversible and site-heterogeneous mixture models.

Main Results:

  • Achieves significant speed improvements, reducing analysis times from months to minutes for large datasets.
  • Enables inferences from hundreds to thousands of taxa on a desktop computer in minutes.
  • Performs probabilistic ancestral sequence reconstruction.

Conclusions:

  • PLEX is a powerful and efficient tool for large-scale phylogenetic analyses with complex evolutionary models.
  • The software's speed and scalability facilitate advanced evolutionary research.
  • Future versions will incorporate advanced features for co-evolution and hypothesis testing.