Summer School on Big Data for Biology
Introduction to Phylogenomic Analysis
May 19-22, 2014
1:30-4:30 PM
GDC 4.302


The summer school on Introduction to Phylogenomic Analysis will provide a survey of phylogenomic pipelines, and then hands-on training in the use of new software for several steps in the pipeline. Participants will bring their laptops and download software for each tutorial in advance.

This summer school session will teach both basic and advanced material in multiple sequence alignment, phylogenetic tree estimation, and phylogenetic network estimation. Students will learn how to compute multiple sequence alignments and trees using PASTA, and to use Phylonet (a software suite) to estimate phylogenetic trees and networks from multiple gene trees. They will also learn how to compute trees from sequence datasets that contain a mixture of full-length and fragmentary sequences, and to add sequences into a tree, using SEPP.

All students should be sure to download, install, and test all the software (PASTA, Phylonet, and SEPP) well in advance of the course. Some of these programs may not run on Windows, or on older machines with smaller amounts of memory. Please make sure to run the software on some datasets (either datasets provided with the software, or your own). Report problems with installing and running the software no later than Thursday, May 15.

Also: please send an email to the course instructors (Yun Yu, Siavash Mirarab, Tandy Warnow, and Luay Nakhleh) with information about the laptop you will bring, the operating system (e.g., OS X, version 10.8.5), and the amount of available memory. This will help us prepare for the tutorials.