2024 W. Main Street, Suite A200
Durham, NC 27705-4667
Tel: (919) 668-4551
Fax: (919) 668-9198

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Students should have a working knowledge of phylogenetics (maximum parsimony, maximum likelihood, bayesian inference, neighbor-joining) including an understanding of substitution models. The MBL Workshop on Molecular Evolution, or the BML Workshop in Applied Phylogenetics, or equivalent course or experience should suffice. In terms of computing, we expect students to have at least a basic familiarity with Perl, and a basic familiarity with unix shell interface and commands. We recommend that novices have read these books ahead of time:

Perl Students: There are numerous books on perl, though many focus on CGI scripting and do not encourage best practices in terms of modularity and object-oriented design. A good beginner book is Mastering Perl for Bioinformatics by James Tisdal ISBN: 0596003072. Also consider reading Perl How To Program, by H.M. Deitel, P.J. Deitel, T. Nieto and D.C. McPhie ISBN:0130284181.

SQL: Students should introduce themselves to SQL by reading an introductory book on the subject. We also recommend the following book on storing trees in databases: Celko, Joe. 2004. Joe Celko’s Trees and Hierarchies in SQL for Smarties. Elsevier, San Francisco.

For simplicity, efficiency, and continuity, we will be using Apple Macintosh notebook computers or Linux computers.

Each student is strongly encouraged to bring her or his own Apple Macintosh iBook, MacBook (or equivalent) running OSX 10.4, 10.5, or 10.6 with Apple’s developer package installed; or a computer running Linux with a working wireless card installed, superuser control, and Perl, PostgreSQL, and DBD/DBI installed with a functioning CPAN installer. If you cannot bring one, a computer will be provided. Bringing your own computer has the advantage that you will leave the course with a machine loaded and configured with a working set of phyloinformatic libraries, programs, and modules.