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

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Published on: August 16, 2017

Phylogenetic analysis of protein sequence data using the Randomized Axelerated Maximum Likelihood (RAXML) Program.

Antonis Rokas1

  • 1Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.

Current Protocols in Molecular Biology
|October 12, 2011
PubMed
Summary
This summary is machine-generated.

This study reviews phylogenetic analysis principles for protein sequences. It details standard methods using the RAXML program for evolutionary relationship studies.

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Area of Science:

  • Bioinformatics
  • Evolutionary Biology
  • Computational Biology

Background:

  • Phylogenetic analysis investigates evolutionary relationships among biological entities.
  • It is crucial in comparative sequence analysis, particularly for protein sequences.
  • Understanding protein evolution and function relies heavily on these analyses.

Purpose of the Study:

  • To provide a foundational review of phylogenetic analysis principles.
  • To describe standard phylogenetic analyses applicable to protein sequence data.
  • To demonstrate the application of the RAXML program in these analyses.

Main Methods:

  • Review of established phylogenetic analysis principles.
  • Description of common phylogenetic analysis techniques for protein sequences.
  • Practical demonstration using the RAXML (Randomized Axelerated Maximum Likelihood) program.

Main Results:

  • A clear overview of phylogenetic analysis concepts.
  • Detailed explanation of RAXML program usage for phylogenetic inference.
  • Illustrative examples of protein sequence phylogenetic analyses.

Conclusions:

  • Phylogenetic analysis is a key tool for studying protein evolution.
  • The RAXML program offers a robust method for phylogenetic analysis of protein data.
  • This unit serves as a guide for researchers applying these methods.