Software School on New Methods for Phylogenomics and Metagenomics
Co-located with Evolution 2014
Raleigh Convention Center, NC
Rooms 302A-C
June 20, 2014
8:30 AM - 2:45 PM

Tutorials

The software school on new methods for phylogenomics and metagenomics will provide hands-on training in the use of new software. Participants bring their laptops and download software for each tutorial in advance. Each tutorial will last approximately 75 minutes.

Schedule

• 8:30-9:45: Tutorial 1 (Multiple Sequence Alignment), Rooms 302A and 302B.
• 9:45-10:15 Break
• 10:15-11:45: Tutorials 3 (GARLI, 302A), 6 (Phyldog, 302B), and 7 (MulRF, 302C)
• 11:45-1:15 Lunch
• 1:15-2:30: Tutorials 5 (ASTRAL, 302A and 302B) and 9 (HMMER, 302C)
• 2:30-3:45: Tutorials 2 (BAli-Phy, 302C), 4 (Phylonet, 302B), and 8 (Metagenomics, 302A)

List of tutorials

• Tutorial 1: Large-scale multiple sequence alignment
  • We will teach PASTA, a new method for co-estimating multiple sequence alignments and phylogenetic trees. It is a direct improvement of SATé (Science 2009): it is more accurate on large datasets and can analyze much larger datasets - up to 200,000 sequences). PASTA uses almost the identical GUI as SATé even if you are an experienced SATé user, this will be a useful tutorial. Taught by Siavash Mirarab (Texas). See this page.
• Tutorial 2: BAli-Phy
  • BAli-Phy, a method that co-estimates sequence alignments and trees using MCMC, taught by Ben Redelings. Please download and install BAli-Phy before coming to the tutorial. Here are links to the Manual and Tutorial.
• Tutorial 3: GARLI
  • GARLI a program for maximum likelihood estimation of phylogenetic trees from sequence alignments, developed by Derrick Zwickl. GARLI is currently being revised to enable more sensitive treatment of indels, and the tutorial will provide training in these new capabilities. Taught by Derrick Zwickl or Mark Holder. Click here for the tutorial materials.
• Tutorial 4: Phylonet
  • Phylonet is a software suite for estimating species trees and networks under conditions where gene trees can differ from the species tree due to incomplete lineage sorting and hybridization. The tutorial on how to use Phylonet will be taught by Yun Yu (Rice). See the following webpages:
    • Tutorial Presentation (PDF),
    • Tutorial (HTML), and
    • Webpage with downloadable software.
• Tutorial 5: ASTRAL, species tree estimation under the multi-species coalescent
  • We will cover coalescent-based estimation of species trees, and teach a tutorial for ASTRAL (new coalescent-based method, developed by Mirarab et al., to appear in Bioinformatics). Instructors include Md. S. Bayzid and Siavash Mirarab, from Texas.
• Tutorial 6: Phylodog
  Phyldog, a method for co-estimating gene trees and species trees from sequence alignments, under a duplication/loss scenario, taught by Bastien Boussau
• Tutorial 7: MulRF
  MulRF, software by Ruchi Chaudhary for computing a species tree that is close (under the Robinson-Foulds distance) to the input gene trees. See also the paper on MulRF.
• Tutorial 8: Metagenomic analysis and phylogenetic analysis of datasets containing fragmentary sequences
  • SEPP, "SATe-enabled phylogenetic placement" (software for multiple sequence alignment and phylogenetic analysis of fragmentary sequences), and TIPP (taxonomic identification and phylogenetic profiling), taught by Siavash Mirarab (Texas) and Nam-Phuong Nguyen (Texas). See this page for the SEPP tutorial.
• Tutorial 9: HMMER
  • HMMER, a suite of tools focused on building and using Hidden Markov Models, developed by Sean Eddy (HHMI) and his group. This tutorial will be taught by Travis Wheeler, from Sean Eddy's group at HHMI Janelia Farm Research Campus. Please visit this page and follow directions to ensure that you have HMMER installed prior to the tutorial.

Registration is required, but participation in both the symposium and workshop is free for SSB members. Travel awards are available for students, postdocs, and assistant professors; see this webpage for more information.