2015 Phylogenomics Symposium and Software School
Undergrad Science Building, The University of Michigan at Ann Arbor
May 18 and 19, 2015
(schedule)

This symposium and software school immediately precedes the Standalone meeting of the Society for Systematic Biology, at the University of Michigan at Ann Arbor.

The Symposium and Software School will take place at the Undergrad Science Building (USB); the Symposium will take place in room USB 2260, and the Software School will take place in rooms USB 2244 and USB 1250.

This symposium and workshop is sponsored by the National Science Foundation through grant DBI-1461364 to the University of Illinois at Urbana-Champaign.

The Symposium (May 18, 1-5 PM, USB 2260) will feature talks by the developers of new software, including:

• Tandy Warnow: New methods for estimating very large multiple sequence alignments and trees with up to 1,000,000 sequences (PPTX) (PDF)
• Siavash Mirarab: New methods for estimating species trees in the presence of gene tree incongruence due to incomplete lineage sorting, and applications in the Thousand Plant Transcriptome Project and the Avian Phylogenomics Project,
• Luay Nakhleh: New methods for estimating phylogenetic networks in the presence of gene tree incongruence due to horizontal gene transfer, hybrid speciation, and incomplete lineage sorting,
• Nam Nguyen: Taxonomic identification of metagenomic data (PPT) (PDF)
• Laura Kubatko Efficient estimation of species-level phylogenies using genome-scale data

The Software School (May 19, 9 AM - 2:30 PM, USB 2244 and USB 1250) will provide hands-on training in new software tools:

• PASTA: co-estimation of multiple sequence alignments and trees with up to one million sequences (webpage) (paper) (tutorial)
• UPP: multiple sequence alignment of up to one million sequences, including datasets with fragmentary sequences (github) (tutorial)
• ASTRAL: Methods for estimating species trees from gene trees in the presence of incomplete lineage sorting (github) (paper) (tutorial)
• Phylonet: Methods for estimating phylogenetic networks from multiple gene trees (webpage) (tutorial)
• TIPP: Taxonomic identification and phylogenetic profiling of metagenomic data (github) (paper) (tutorial)
• SVDquartets: a method for computing species trees on four species from gene sequences in the presence of incomplete lineage sorting (webpage) (PAUP* download)

Please download, install, and run all software before the software school. Please contact Tandy Warnow (warnow@illinois.edu) for more information.

To register (whether or not you wish to apply for a travel award), please download and fill out the application form, and send it to Tandy Warnow at warnow@illinois.edu. Note that registration for this symposium is separate from the registration for the SSB Standalone meeting! Also, there is no cost to attend this meeting.

Travel awards (supported by NSF) of up to $500 are available to graduate students, postdocs, and faculty who wish to attend the software school and symposium. (Important: the travel award is only for reimbursement of expenses directly related to attending the Symposium and Software School; that means at most three nights (May 17-19) of lodging and round-trip travel to Ann Arbor, Michigan. If you plan to attend the SSB Standalone meeting and need additional support, please contact the organizers of that meeting for information on how to apply for additional funds.)