Software School on New Methods for
Phylogenomics and Metagenomics
Co-located with Evolution 2014
Raleigh Convention Center, NC
June 20, 2014
8:30 AM - 2:45 PM
The software school on new methods for
phylogenomics and metagenomics will provide
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.
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)
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
new method for co-estimating
multiple sequence alignments and phylogenetic
trees. It is a direct improvement of SATé (Science 2009):
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).
- Tutorial 2: BAli-Phy
- Tutorial 3: 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.
here for the tutorial materials.
- Tutorial 4: 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).
the following webpages:
- Tutorial 5: ASTRAL, species tree estimation under the
- 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).
Md. S. Bayzid and Siavash Mirarab, from Texas.
- Tutorial 6: Phylodog
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
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
- 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.
this page and follow
directions to ensure that you have HMMER installed prior to the
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.