Syllabus
 
All students take the Mesquite, HyPhy, and SQL modules. Students choose between either the java modules (yellow) or the perl modules (green). Additional information on material covered can be found here.
Mesquite Scripting Language 1. Interface, language, syntax 2. Designing Work-flows 3. Biological Topics HyPhy Scripting Language 1. Interface, language, syntax 2. Standard analyses; workflow integration 3. Designing HyPhy scripts 4. HyPhy for server applications Java Route 1. Basic Concepts 2. PAL, JEBL, biojava libraries 3. Writing a Mesquite Module Perl Route 1. BioPerl installation and use 2. Bio::Phylo 3. Perl interface into CIPRES SQL and BioSQL 1. Introduction to databases and queries 2. Storing and querying trees 3. BioSQL overview, installation, use JDBC Interface to MySQL Perl DBI Interface to MySQL