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In the previous course in the Specialization, we learned how to compare genes, proteins, and genomes. One way we can use these methods is in order to construct a "Tree of Life" showing how a large collection of related organisms have evolved over time. In the first half of the course, we will discuss approaches for evolutionary tree construction that have been the subject of some of the most cited scientific papers of all time, and show how they can resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans. In the second half of the course, we will shift gears and examine the old claim that birds evolved from dinosaurs. How can we prove this? In particular, we will examine a result that claimed that peptides harvested from a T. rex fossil closely matched peptides found in chickens. In particular, we will use methods from computational proteomics to ask how we could assess whether this result is valid or due to some form of contamination. Finally, you will learn how to apply popular bioinformatics software tools to reconstruct an evolutionary tree of ebolaviruses and identify the source of the recent Ebola epidemic that caused global headlines.

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  • Week 1 - Week 1: Introduction to Evolutionary Tree Construction

    Welcome to our class!

    In this class, we will consider the following two central biological questions (the computational approaches needed to solve them are shown in parentheses):

    1. Weeks 1-3: Which Animal Gave Us SARS? (Evolution...
    2. Week 2 - Week 2: More Algorithms for Constructing Trees from Distance Matrices

      Welcome to Week 2 of class!

      Last week, we started to see how evolutionary trees can be constructed from distance matrices.  This week, we will encounter additional algorithms for this purpose, including the neighbor-joining algorithm, which has...

    3. Week 3 - Week 3: Constructing Evolutionary Trees from Characters

      Welcome to week 3 of class!

      Over the last two weeks, we have seen several different algorithms for constructing evolutionary trees from distance matrices.

      This week, we will conclude the current chapter by considering what happens if we use ...

    4. Week 4 - Week 4

      Welcome to week 4 of the class!

      Did birds evolve from dinosaurs? Over the next two weeks, we will see how we could analyze molecular evidence in support of this theory. You can find this week's Bioinformatics Cartoon from Randall Christopher at the ...

    5. Week 5 - Week 5: Resolving the T. rex Peptides Mystery?

      Welcome to week 5 of class!

      Last week, we asked whether it is possible for dinosaur peptides to survive locked inside of a fossil for 65 million years. This week, we will see what this question has to do with statistics; in the process, we will see ...

    6. Week 6 - Week 6: Bioinformatics Application Challenge

      Welcome to the sixth and final week of the course!

      In this week's Bioinformatics Application Challenge, we will use reconstruct an evolutionary tree of ebolaviruses and use it to determine the origin of the pathogen that caused the recent outbreak i...



Pavel Pevzner
Department of Computer Science and Engineering

Phillip Compeau
Visiting Researcher
Department of Computer Science & Engineering



University of California, San Diego
UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory.



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