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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...
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...
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...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PALM: a paralleled and integrated framework for phylogenetic inference with automatic likelihood model selectors.

Shu-Hwa Chen1, Sheng-Yao Su, Chen-Zen Lo

  • 1Institute of Information Science, Academia Sinica, Taipei, Taiwan.

Plos One
|December 10, 2009
PubMed
Summary

The PALM framework simplifies phylogenetic analysis by automating model selection and tree topology derivation. This tool enhances efficiency and accessibility for researchers, reducing computational complexity.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic analysis requires selecting appropriate substitution models and deriving tree topologies, which is computationally intensive and requires expertise.
  • Current methods involve tedious manipulation of multiple separate programs, hindering efficiency and thoroughness.

Purpose of the Study:

  • To present an intuitive framework, Phylogenetic Reconstruction with Automatic Likelihood Model selectors (PALM), for seamless phylogenetic analysis.
  • To provide a best-fit model selection mechanism and updated algorithms for efficient phylogenetic reconstruction.

Main Methods:

  • PALM integrates ClustalW, PhyML, MODELTEST, and ProtTest, evaluating 56 nucleotide and 112 protein substitution models.
  • It utilizes task parallelism with MPICH2/PhyML and a job controller for accelerated maximum likelihood and bootstrapping computations.
  • An interactive web component, PalmTree, facilitates tree visualization and manipulation.

Main Results:

  • PALM offers a user-friendly interface for submitting sequences and retrieving phylogenetic analysis results.
  • The framework effectively addresses the computational challenges of maximum likelihood methods.
  • It provides statistical methods for model selection and bootstrapping, reducing calculation time for large datasets.

Conclusions:

  • PALM streamlines phylogenetic reconstruction, making complex analyses accessible to researchers without specialized expertise.
  • The framework enhances efficiency and reduces computation time, particularly for large datasets.
  • PALM is available online at http://palm.iis.sinica.edu.tw.