UNIT 6.6 Maximum-Likelihood Analysis Using TREE-PUZZLE

  1. Heiko A. Schmidt,
  2. Arndt von Haeseler

Published Online: 1 MAR 2007

DOI: 10.1002/0471250953.bi0606s17

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Schmidt, H. A. and von Haeseler, A. 2007. Maximum-Likelihood Analysis Using TREE-PUZZLE. Current Protocols in Bioinformatics. 17:6.6:6.6.1–6.6.23.

Author Information

  1. Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), Vienna, Austria; University of Vienna, Austria; Medical University Vienna, Austria; University of Veterinary Medicine, Vienna, Austria

Publication History

  1. Published Online: 1 MAR 2007
  2. Published Print: MAR 2007


TREE-PUZZLE provides a means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e., groups of four sequences. Basic Protocol 1 explains how to reconstruct trees based on the maximum-likelihood principle and quartet puzzling. Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol 3 explains how to compare tree topologies using different tests.


  • evolutionary tree;
  • phylogeny reconstruction;
  • tree-puzzle;
  • visualizing phylogenetic content;
  • comparing trees