Unit

UNIT 19.11 Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program

  1. Antonis Rokas

Published Online: 1 OCT 2011

DOI: 10.1002/0471142727.mb1911s96

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Rokas, A. 2011. Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program. Current Protocols in Molecular Biology. 96:19.11:19.11.1–19.11.14.

Author Information

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

Publication History

  1. Published Online: 1 OCT 2011
  2. Published Print: OCT 2011

Abstract

Phylogenetic analysis is the study of evolutionary relationships among molecules, phenotypes, and organisms. In the context of protein sequence data, phylogenetic analysis is one of the cornerstones of comparative sequence analysis and has many applications in the study of protein evolution and function. This unit provides a brief review of the principles of phylogenetic analysis and describes several different standard phylogenetic analyses of protein sequence data using the raxml (Randomized Axelerated Maximum Likelihood) Program. Curr. Protoc. Mol. Biol. 96:19.11.1-19.11.14. © 2011 by John Wiley & Sons, Inc.

Keywords:

  • molecular evolution;
  • bootstrap;
  • multiple sequence alignment;
  • amino acid substitution matrix;
  • evolutionary relationship;
  • systematics