File decompression software, such as Winzip® or StuffIt®, is required to open the .tar files found in this section. Any text editor can be used to view the .fas and .fasta files found in this section.

Below is a tentative schedule of laboratory assignments for the course. Note that each laboratory will generally consist of (1) a set of background readings on the biological and computational theory behind the assignment; (2) a set of 'warm-up' preparatory exercises to gain familiarity with the software and the assignment domain, perhaps including some non-computer problems; and (3) the main assignment itself, which will be computer-based. Instructions for using the software for each laboratory will be provided. Most of the programs and all the data will be available for download to PCs, Macs, and Linux®-based systems.

  • Goals. The aim of the lab work is to make sure that you get a chance to apply the theory to real data. We can talk and talk about evolutionary models, but in our experience, getting your hands dirty may be the best way to learn.
  • Mechanics. In general, the labs will involve computer work with modeling and application to ‘live’ data sets. The computational models and data will always be available to either download to your own computer (either PC, Macintosh®, or Linux® box), with the data available on the course website.  During the latter part of the course, we can use this time to talk about projects.
  • Format. Each lab will be divided into three parts: first, a ‘warmup’ section to get familiar with the computational tools; second, brief questions that review and extend the lecture material; and third, a substantive application to a real data set drawn from the literature. We anticipate that each laboratory will take about two weeks, unless otherwise noted. In general, you won’t need to do your own programming in C++, Perl, Java®, etc. – rather, we will use off-the-shelf tools. However, some questions and projects later on may require some elementary skills with manipulating data, that you should be able to do via Perl, or Matlab® – almost any such set of tools. If you find that challenging, do not despair. Please just talk to me: we can team up people that have complementary skill sets, or substitute alternative questions, etc.
  • Lab reports. We will strive to make this a ‘paperless’ class. Lab reports should be written up as web pages, with the final URL sent to professor.
  • Policy on cooperative work. We strongly encourage cooperation. You are free to work in groups, but please do write up your lab yourself (however, the Final Project is a team effort and requires only one write-up)

Laboratory Assignments

Lab 1: Forces of Evolution HWwarmup (PDF)
lab1part2 (PDF)
Lab 2: Evolution and Genomics

falciparum (FAS)
pf11_0344 (FASTA)
Pfa3D7_chr11ORFs50 (FASTA)
lyzC (TXT)
paml_gstd1_codeml.ctl (TXT)
paml_gstd1_seqfile (TXT)
paml_ldh_codeml.ctl (TXT)
paml_ldh_seqfile (TXT)
paml_ldh_tree.H0 (TXT)
paml_ldh_tree.H1 (TXT)
paml_ldh_tree.H2 (TXT)
paml_ldh_tree.H3 (TXT)
paml_readme (TXT)
genes (TAR)
chr2 (TAR)