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Chapter 14: Reconstructing Evolutionary Trees Destinations

Explore key concepts and research through these links to additional web resources.

14.1 The Logic of Phylogeny Inference

• Phylogeny
  From KISAC Bioinformatics in Sweden, this site provides an excellent overview of the process of inferring phylogeny from molecular sequence data, with reference to the various computer programs available for use.
  Keywords: phylogeny, genetics, bioinformatics

• HIV Database: phylogenetic tree tutorial
  This is a step-by-step tutorial for inferring phylogeny from molecular data, provided by the HIV Sequence Database project of the Los Alamos National Laboratory. From the tutorial, you can also link to the next site.
  Keywords: phylogenetic trees, HIV, genomic research

• Cladistics
  Part of the University of California, Berkeley's Museum of Paleontology website, this site offers a good, moderately technical discussion of the process of cladistic analysis.
  Keywords: cladistics, paleontology, analysis

14.2 The Phylogeny of Whales

• Cows and Hippos and Whales, OH MY!
  This abstract reviews the analysis of mitochondrial DNA regions in the sperm whale to better understand its phylogenetic placement.
  Keywords: whales, phylogeny, genetic analysis

14.3 Using Phylogenies to Answer Questions

• PHYLIP Home Page
  Joseph Felsenstein's PHYLIP is a set of computer programs for inferring phylogeny. Analytical algorithms include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.
  Keywords: PHYLIP, phylogeny, gene sequences

• Phylogeny Programs
  Dr. Felsenstein also provides a page with links to a wealth of other phylogeny programs.
  Keywords: phylogeny programs, genetic analysis, evolutionary trees