Current Funding

NSF DEB 0733029

Large-Scale Simultaneous Multiple Alignment and Phylogeny Estimation
webpage
PI: Warnow. Co-PI: Linder.
Collaborators: University of Georgia, University of Kansas, University of Nebraska
2007-2012, $1.7 Million

NSF DBI-1062335

Novel Methodologies for Genome-scale Evolutionary Analysis of Multi-locus data
webpage
PI: Warnow. Co-PI: Linder.
Collaborators: Rice University (Luay Nakhleh, PI) and Stanford University (Noah Rosenberg, PI), 2011-2014.
Rice University, Stanford University, and the University of Texas at Austin were awarded collaborative grants to develop and implement algorithms and software tools for the analysis of gene genealogies and inference of species phylogenies from them. A gene genealogy, also known as a gene tree, models how genes replicate and get transmitted from one generation to the next during evolution. A species phylogeny models how species arise and diverge. A species phylogeny is traditionally inferred by a three-step process: (1) a genomic region from the set of species under study is sequenced; (2) a "gene tree" is inferred for the genomic region; and, (3) the gene tree is declared to be the species tree. However, recent evolutionary genomic analyses of various groups of organisms have demonstrated that different genomic regions may have evolutionary histories that disagree with each other as well as with that of the species. Further, evolutionary processes such as horizontal gene transfer, result in network-like, rather than tree-like, species phylogenies. This joint project will develop accurate computational methods for determining the causes of gene tree discordance, and inferring species phylogenies (trees as well as networks) from gene trees despite their discordance. Special emphasis will be put on the efficiency of the methods so that they allow for analysis of genome-scale data sets. All methods will be implemented and extensively tested for performance.

Recent Funding

John Simon Guggenheim Memorial Foundation Fellowship

Three new problems in evolutionary tree estimation: whole genome phylogeny, co-estimation of sequence alignments and phylogenetic trees, and metagenomic phylogenetic placement (see this page).

NSF ITR 0331453

• Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics
  PI: Warnow. Collaborators: Florida State University, UC Berkeley, UC San Diego, University of New Mexico
  2003-2010, $11.6 Million
  CIPRES webpage

NSF ITR BCS 0312830

• Algorithms for Inferring Reticulate Evolution in Historical Linguistics
  PI: Warnow, PI at the University of Pennsylvania (collaborating institution) Donald Ringe
  Collaborators: Rice University, UC Berkeley, University of Pennsylvania
  2003-2009, $344,517
  Computational Phylogenetics for Historical Linguistics webpage

NSF IGERT DGE 0114387

• Computational Phylogenetics and Applications to Biology
  PI: Hillis, Co-PIs Warnow, Jansen, and Gutell, 2001-2007. Total amount $2,741,575.

NSF DEB 0120709

• Comparative Chloroplast Genomics: Integrating Computational Methods, Molecular Evolution, and Phylogeny.
  PI: Robert Jansen, Co-PIs Warnow and Raubeson, 2001-2007. Total amount: $1,350,000.

NSF ITR/AP 0121680

• Reconstructing Complex Evolutionary Histories
  Collaborators: University of New Mexico
  2001-2009, $1,707,458
  Complex Evolution Project webpage