Bioinformatics and Functional Genomics, 2nd Edition

Chapter 7: Molecular Phylogeny and Evolution

This page offers the web documents that are referred to in Chapter 7 of the book. In Chapter 6 we discussed multiple sequence alignments. These can be visualized as phylogenetic trees. We describe the main features of a tree (topology and branch lengths) and the stages of generating a tree. Approaches include maximum parsimony, distance-based methods, maximum likelihood, and Bayesian inference of phylogeny.

Web documents Description
Web Document 7-1 13 globin protein sequences
Web Document 7-2 Globin evolution from Zuckerkandl and Pauling (1962)
Web Document 7-3 12 aligned myoglobin DNA coding sequences (plus cytoglobin)
Web Document 7-4 vertebrate globins (used to make an HMM)
Web Document 7-5 Test for positive or negative selection using MEGA software
Web Document 7-6 Eleven randomly selected protein sequences used for phylogenetic analysis
Web Document 7-7 Output file from the ModelTest program in which 56 models of nucleotide substitution were evaluated for a set of myoglobins
Web Document 7-8 Phylogenetic analysis of 13 globins using TreePuzzle : maximum likelihood inference of phylogeny
Web Document 7-9 TreePuzzle output
Web Document 7-10 Bayesian inference of phylogeny: 13 globins using MrBayes
Web Document 7-11 Bayesian inference of phylogeny: MrBayes output
Web Document 7-12 Six primate mitochondrial DNA sequences (nexus format)
Web Document: Table 7.1 Example of the UPGMA method of tree construction

Chapter 7 Resources
Powerpoint of the phylogeny lecture (December 2008)(December 2009/January 2010)
PDF (black & white) of the handout for printing, 6 slides per page (December 2008)
Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests
Computer lab (coming soon)
Audio file of a phylogeny lecture (December 2008)(January 2010)
Key URLs: Joseph Felsenstein's list of phylogeny links; MEGA website; LANL HIV sequence database with tutorial; MrBayes; PHYLIP; PAUP; TreePuzzle.

Chapter 7 errata
Page 261, legend to Fig. 7.28 Text should read: “However, columns having entirely conserved residues (filled arrowheads) are not informative. Columns in which there are at least two different residues that occur at least two times (open arrowheads) are informative.”