Maximum-likelihood analysis using TREE-PUZZLE

Curr Protoc Bioinformatics. 2007 Mar;Chapter 6:Unit 6.6. doi: 10.1002/0471250953.bi0606s17.

Abstract

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.

MeSH terms

  • Computer Graphics
  • Computer Simulation
  • Data Interpretation, Statistical
  • Evolution, Molecular*
  • Likelihood Functions
  • Models, Genetic*
  • Models, Statistical
  • Phylogeny
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • User-Computer Interface*