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Durham, NC 27705-4667
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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 or java or R, and a basic familiarity with unix shell interface and commands. We recommend that novices have read these books ahead of time:

Java Students: Head First Java, 2nd Edition by Kathy Sierra, Bert Bates ISBN: 0596009208. This is a good book for those with no java or programming experience. Alternatively, Thinking in Java (4th Edition) by Bruce Eckel ISBN: 0131872486 is also very good, but assumes some programming experience.

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.

R Students: Students with no R or programming experience should work through An Introduction to R, paying special attention to object (variable) types, reading data from files, and installing and using packages. Additionally, this is recommended reading for phylogenetic tree representation in R. Students may find Analysis of Phylogenetics and Evolution in R to be useful. Students should also generally be familiar with phylogenetic comparative methods (see comparative methods in R wiki at http://r-phylo.org).

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.

Each student is strongly encouraged to bring her or his own Apple Macintosh iBook, MacBook (or equivalent) running OSX 10.4 or 10.5 with Apple’s developer package installed, and with a wireless card installed. If you cannot bring one, we will work to find a machine for loan, but 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.