Workshop: UTexas_Austin.PhylogenomicsMethods.Feb16-17

Workshop: UTexas_Austin.PhylogenomicsMethods.Feb16-17

13 November, 2012

Dear Colleagues,
We are pleased to announce the Symposium/ on New Methods for Phylogenomics and Metagenomics. It will be held on February 16 and 17, 2013, at the University of at Austin.
The symposium (February 16) will feature talks on new methods for

– estimating very large multiple sequence alignments,

– estimating very large phylogenetic trees,

– estimating species trees and networks in the presence of gene tree incongruence due to horizontal gene transfer, gene duplication and loss, or incomplete lineage sorting,

– estimating or correcting estimated gene trees given species trees in the presence of gene duplication and loss scenarios, and

– metagenomic analysis, including estimating phylogenies and multiple sequence alignments from fragmentary sequences and taxon identification of fragmentary sequences.
The current list of speakers at the symposium includes:

Dan Brown (Waterloo), Mark Holder (), Curtis Huttenhower (Harvard, tentative), Manolis Kellis (MIT, tentative), Bret Larget(, tentative), Jim Leebens-Mack (), Luay Nakhleh (Rice), Eric Nawrocki (Janelia Farm, HHMI), Ben Redelings (NESCENT), Sebastien Roch (Wisconsin), and Tandy Warnow(Texas).
The workshop (February 17) will provide tutorials in the use of new methods. Specific software that will be taught includes:

– SATe, co-estimation of multiple sequence alignments and phylogenetic trees, taught by Mark Holder (Kansas) and Siavash Mirarab (Texas),

– SEPP, “SATe-enabled phylogenetic placement” (software for multiple sequence alignment and phylogenetic analysis of fragmentary sequences), taught by Siavash Mirarab (Texas),

– DACTAL, “divide-and-conquer trees (almost) without alignments”,

– SuiteMSA, alignment visualization and analysis software, taught by Etsuko Moriyama (),

– Phylonet, taught by Yun Yu (Rice),

– BAli-Phy, Bayesian co-estimation of alignments and trees, taught by Ben Redelings (Duke),

– Infernal, software by Eric Nawrocki and Sean Eddy (Janelia Farm) for annotating and estimating alignments on 16S rRNA sequences, taught by Eric Nawrocki,

– TreeFix and TreeFix-DTL, software by Mukul Bansal and Manolis Kellis (MIT) for “correcting” gene trees given a species tree, taking gene duplication and loss into account, taught by Mukul Bansal, and

– MetaPhlAn, software for analysis of metagenomic shotgun sequencing data, taught by Eric Franzosa (Harvard).
Registration is required, but participation in both the symposium and workshop is free. Travel awards for up to 50 workshop participants are available; please send an inquiry to Laurie Alvarez ( by November 15, 2012, if you would like to apply for an award.
For the most updated information, please check:
Tandy Warnow, The University of Texas at Austin

Michael Braun, The Smithsonian Institution

Mark Holder, The University of Kansas

Jim Leebens-Mack, The University of Georgia

Randy Linder, The University of Texas at Austin

Etsuko Moriyama, The University of Nebraska – Lincoln

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