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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...
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...
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,...
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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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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

Improved layout of phylogenetic networks.

Philippe Gambette, Daniel H Huson

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |August 2, 2008
    PubMed
    Summary

    This study introduces new algorithms to improve the visualization of split networks used in phylogenetic analysis. These methods enhance network layout clarity and area coverage for better evolutionary insights.

    Area of Science:

    • Phylogenetics and evolutionary biology
    • Computational biology and bioinformatics

    Background:

    • Split networks are increasingly utilized in phylogenetic analysis.
    • Current visualization methods, like the equal angle algorithm, often result in suboptimal layouts.
    • Improved network visualization is crucial for accurate interpretation of evolutionary relationships.

    Purpose of the Study:

    • To address the limitations of existing split network drawing algorithms.
    • To present novel algorithms for enhanced split network visualization.
    • To explore methods for maximizing network area coverage and improving layout clarity.

    Main Methods:

    • Development of an algorithm to maximize the area covered by split networks.
    • Extension of the equal-daylight algorithm for application to split networks.

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  • Investigation of spring embedder algorithms for network layout.
  • Discussion on constructing rooted split networks.

    • Main Results:

    • The proposed algorithms offer improved layouts compared to standard methods.
    • Maximized area coverage leads to more informative visualizations.
    • The extended equal-daylight and spring embedder approaches provide viable alternatives for network drawing.
    • Methods for constructing rooted split networks are detailed.

    Conclusions:

    • The presented algorithms significantly improve the visualization of split networks.
    • Enhanced layouts facilitate better understanding of complex evolutionary histories.
    • These advancements contribute to more effective phylogenetic analysis using split networks.