Workshop on New Methods for
Phylogenomics and Metagenomics
The University of Texas at Austin
February 16 and 17, 2013
Tutorial Schedule
The workshop (February 17, 2013) will provide tutorials
in the use of new methods.
General Schedule:
- 7:30 AM - 8:20 AM, Breakfast
- 8:30 AM - 12:20 PM, Tutorials (three parallel tracks)
- 12:30 PM - 1:20 PM, Lunch
- 1:30 PM - 2:15 PM, Q&A and Discussion with Tutorial Speakers
Detailed schedule (and links to the downloadable software and
written tutorials) for the
three parallel tracks:
- Multiple Sequence Alignment and Phylogeny Estimation (8:30 AM to 12:20 PM) - two locations
- 8:30-9:20, SATé,
co-estimation of multiple sequence alignments and phylogenetic trees (especially
for analyses of datasets with many sequences),
taught by
Mark Holder (Kansas).
See this page for the written tutorial and downloadable software.
Location: Avaya Auditorium (ACE 2.302)
- 9:30-10:20,
BAli-Phy, Bayesian co-estimation of alignments and trees, taught by
Ben Redelings (Duke),
see this page for the workshop tutorial materials.
Location: ACE 2.402
- 10:30-11:20,
SSU-Align and
Infernal,
software
by Eric Nawrocki and Sean Eddy (Janelia Farm) for annotating and estimating alignments on 16S rRNA
seqences, taught by
Eric Nawrocki (HHMI).
See
this page for the downloadable SSU-Align and instructions.
The tutorial is included as part of the SSU-align user's guide,
downloadable from the webpage, and (PDF)
for the workshop tutorial.
Location: ACE 2.402
- 11:30-12:20 SuiteMSA, alignment visualization and analysis software, taught by
Etsuko Moriyama (Nebraska).
See this link, or
this page for the written tutorial and downloadable software.
Location: ACE 2.402
- Species Tree Estimation from Multiple Markers (9:30 AM to 12:20 PM) - Avaya Auditorium
(ACE 2.302)
- 9:30 AM - 10:20 AM,
Phylonet, taught by
Yun Yu (Rice).
See this page for the written tutorial and downloadable software, and
this
(PDF)
for the tutorial presentation.
- 10:30 AM - 11:20 AM,
BUCKy,
software by
Larget, Kotha, Dewey, and Ané, for
species tree estimation in the presence
of incomplete lineage sorting using
Bayesian Concordance Analysis, taught by Bret
Larget.
See this page
for tutorial materials.
- 11:30 AM - 12:20 PM,
*BEAST, Bayesian MCMC co-estimation of
gene trees and species trees, software by Joseph Heled and
Alexei Drummond,
taught by Joseph Heled.
See this page for written tutorial and downloadable software.
- Metagenomic Data Analyses and Gene Tree Correction (9:30 AM to 12:20 PM) -
PAT 141SA
- 9:30 AM - 10:20 AM, SEPP,
"SATe-enabled phylogenetic placement" (software for
multiple sequence alignment and
phylogenetic analysis of fragmentary sequences), taught by
Siavash Mirarab (Texas).
See this page for the written tutorial.
- 10:30 AM - 11:20 AM, MetaPhlAn,
software for analysis of metagenomic shotgun sequencing
data, taught by Eric Franzosa (Harvard),
see this page for written tutorial and downloadable software and
here for the workshop presentation in
PDF format.
- 11:30 AM - 12:20 PM,
TreeFix
and TreeFix-DTL, software by
Mukul Bansal,
Manolis Kellis,
and Yi-Chieh Wu (MIT),
for "correcting" gene trees given a species tree, taking
gene duplication,
horizontal gene transfer, and gene loss into account, taught by Mukul Bansal,
see this page for written tutorial and downloadable software.
Registration is required, but participation in both the symposium and workshop is free.
However,
we are close to the maximum number of registrants, as
already 186 people have registered.
If you would like to attend, please contact Laurie Alvarez
as soon as possible.
The deadline for travel award requests has passed,
and all award decisions have been made. At this time, we will
not to be able to make any new awards.
There are buses between the University of Texas and the Austin Airport;
on Sunday, for example, there is a bus that leaves
the University at 2:52 PM and arrives at the airport at 3:25 PM.
Please see this PDF
for the route and schedule for this bus service (Capital Metro, route 100).