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Related Concept Videos

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.
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.
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.
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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Related Experiment Video

Updated: May 13, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models.

Manuel Gil1, Marcelo Serrano Zanetti, Stefan Zoller

  • 1Department of Computer Science, Swiss Federal Institute of Technology, Zürich, Switzerland. manuel.gil.sci@gmail.com

Molecular Biology and Evolution
|February 26, 2013
PubMed
Summary
This summary is machine-generated.

Phylogenetic inference using codon models, which better represent protein-coding genes, is now feasible. CodonPhyML offers a fast and versatile maximum likelihood package for accurate evolutionary analysis.

Keywords:
codon modelevolutionmaximum likelihoodphylogeny inferenceselection

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Related Experiment Videos

Last Updated: May 13, 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

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 inference accuracy relies on realistic models of sequence evolution.
  • Codon models offer a more accurate representation of protein-coding genes than nucleotide or amino acid models.
  • Previous codon models were computationally challenging, limiting their application in phylogeny reconstruction.

Purpose of the Study:

  • To present CodonPhyML, a fast maximum likelihood (ML) package for phylogenetic inference using codon models.
  • To provide a comprehensive framework for model selection, including DNA, amino acid, and a wide variety of codon models.

Main Methods:

  • Development of a fast ML package, CodonPhyML, for phylogenetic inference.
  • Implementation of hundreds of different codon models, the largest variety to date.
  • Integration of recent fast methods for estimating phylogenetic branch supports.

Main Results:

  • CodonPhyML demonstrates excellent speed and convergence properties on simulated and real data.
  • The package facilitates accurate phylogenetic inference under codon models.
  • CodonPhyML offers a broad selection of codon models for diverse evolutionary analyses.

Conclusions:

  • CodonPhyML overcomes previous computational limitations, making codon model-based phylogenetic inference practical.
  • The package provides a powerful and efficient tool for evolutionary biologists.
  • CodonPhyML enhances the accuracy and scope of phylogenetic analyses for protein-coding genes.