Completed Funding since 2001

NSF ABI: 1458652

  • New methods for multiple sequence alignment with improved accuracy and scalability
    PI: Tandy Warnow
    August 2015 - July 2021.
    This project developed new methods for multiple sequence alignment, building on our SATé, PASTA, and UPP methods.

NSF CCF: 1535977

  • Graph-Theoretic Algorithms to Improve Phylogenomic Analyses
    Multi-institutional webpage
    Lead Institution: Illinois (PI: Warnow, Co-PI: Chandra Chekuri)
    Collaborative Institution: Berkeley (PI: Satish Rao)

NSF IIS: 1513629

  • Scalable and Highly Accurate Methods for Metagenomics.
    Multi-institutional webpage
    Lead Institution: Illinois (PI: Tandy Warnow)
    Collaborative Institution: University Maryland (PI: Mihai Pop)

NSF DBI-1062335/1461364

  • Novel Methodologies for Genome-scale Evolutionary Analysis of Multi-locus data
    • PI: Luay Nakhleh (Rice University), Co-PIs Noah Rosenberg (Stanford) and Tandy Warnow (Illinois)
    • Illinois webpage
    PI: Warnow.
    Collaborators: Rice University (Luay Nakhleh, PI) and Stanford University (Noah Rosenberg, PI), 2011-2014 (no-cost extensions to 2016).
    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.

John Simon Guggenheim Memorial Foundation Fellowship

  • The fellowship (2010-2011) was awarded for the Computer Science field of study, and addresses three problems in evolutionary tree estimation: whole genome phylogeny, co-estimation of sequence alignments and phylogenetic trees, and metagenomic phylogenetic placement (see this page).

NSF DEB 0733029

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

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


  • 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