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A Protocol for Phylogenetic Reconstruction.

Soham Sengupta1, Rajeev K Azad2,3

  • 1Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 17, 2021
PubMed
Summary
This summary is machine-generated.

This study details reconstructing phylogenetic trees using a maximum-likelihood approach. It aids in understanding evolutionary relationships and gene family evolution through genomic data analysis.

Keywords:
Maximum-likelihoodPhylogenetic analysisPhylogenetic reconstructionPhylogenetic tree

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Genomics

Background:

  • Organismal similarities in biological functions and molecular mechanisms suggest a common evolutionary origin.
  • Phylogenetic analysis, utilizing DNA, RNA, and protein data, is crucial for inferring evolutionary relationships and understanding gene family evolution.
  • Advances in DNA sequencing have led to an exponential growth in genomic data, enabling large-scale reconstruction of the tree of life.

Purpose of the Study:

  • To describe a protocol for reconstructing phylogenetic trees.
  • To illustrate the identification of orthologs and paralogs within gene families.
  • To demonstrate the application of evolutionary insights to gene function.

Main Methods:

  • Utilizing a maximum-likelihood approach for phylogenetic tree reconstruction.
  • Employing a suite of publicly available bioinformatics programs.
  • Analyzing an example dataset to showcase the protocol's effectiveness.

Main Results:

  • Successfully reconstructed a phylogenetic tree from the example dataset.
  • Demonstrated the identification of orthologs and paralogs.
  • Provided a practical workflow for evolutionary analysis.

Conclusions:

  • The described protocol offers a robust method for phylogenetic tree reconstruction.
  • This approach facilitates the study of evolutionary relationships and gene family diversification.
  • Publicly available tools enable accessible and effective phylogenetic analysis.