Bioinformatics and Functional Genomics 3rd Edition

Chapter 15: The Tree of Life

In the last third of this book we explore the tree of life from a genomics perspective. Chapter 15 includes the following:

  • An overview of the history of life on earth, and a description of bioinformatics approaches to making a tree of life
  • A chronological survey of genome sequencing projects
  • A description of genome sequencing
  • We'll explore the Trace Archive for raw data
  • We'll learn how to use Velvet for genome assembly, and Mauve to compare assemblies
  • An overview of how genomes are annotated, including the Ensembl and NCBI pipelines and standards for annotation


For classes on genomics, I recommend that you look at Web Document 15.1 which presents five perspectives on genomics. Students can select a genome of any favorite organism and analyze it in depth according to these organizing principles. As an alternative project, students can select a favorite gene and analyze it across many genomes (see Web Document 15.2).


The WebLinks are all referred to in the chapter. Some of the key URLs we'll encounter include: NCBI; UCSC Genome Browser; Ribosomal Database Project at Michigan State University; Pfam (Protein Family Database); MEGA phylogeny software.