Unit

UNIT 11.3 Beyond Simple Homology Searches: Multiple Sequence Alignments and Phylogenetic Trees

  1. Rebecca A. Zufall

Published Online: 1 JUN 2009

DOI: 10.1002/9780470089941.et1103s01

Current Protocols Essential Laboratory Techniques

Current Protocols Essential Laboratory Techniques

How to Cite

Zufall, R. A. 2009. Beyond Simple Homology Searches: Multiple Sequence Alignments and Phylogenetic Trees. Current Protocols Essential Laboratory Techniques. 1:11.3:11.3.1–11.3.17.

Author Information

  1. University of Houston, Houston, Texas

Publication History

  1. Published Online: 1 JUN 2009
  2. Published Print: JUN 2009

This is not the most recent version of the article. View current version (2 MAY 2017)

Abstract

Phylogenetic trees represent hypotheses about evolutionary relationships between organisms or nucleotide or amino acid sequences. Because the best BLAST hit often does not represent the most closely related sequence, phylogenetic analyses are an essential extension of inquiry into any new protein or gene. In this unit, the reader will first learn how to create a multiple sequence alignment using ClustalX. He or she will then learn how to use that alignment to build a neighbor-joining phylogeny using the program Geneious. Finally, the user will learn how to interpret the phylogeny in light of the research questions. Curr. Protoc. Essential Lab. Tech. 1:11.3.1-11.3.17. © 2009 by John Wiley & Sons, Inc.

Keywords:

  • phylogeny;
  • alignment;
  • neighbor-joining;
  • homology;
  • ClustalX;
  • Geneious