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  1. No Access

    Chapter and Conference Paper

    Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis

    Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic re...

    Ruchi Chaudhary, David Fernández-Baca… in Algorithms for Computational Biology (2015)

  2. No Access

    Chapter and Conference Paper

    GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches

    Gene tree parsimony (GTP) problems infer species supertrees from a collection of rooted gene trees that are confounded by evolutionary events like gene duplication, gene duplication and loss, and deep coalesce...

    Paweł Górecki, J. Gordon Burleigh… in Bioinformatics Research and Applications (2012)

  3. No Access

    Chapter and Conference Paper

    Algorithms for Knowledge-Enhanced Supertrees

    Supertree algorithms combine smaller phylogenetic trees into a single, comprehensive phylogeny, or supertree. Most supertree problems are NP-hard, and often heuristics identify supertrees with anomalous or unw...

    André Wehe, J. Gordon Burleigh… in Bioinformatics Research and Applications (2012)

  4. No Access

    Chapter and Conference Paper

    Fast Local Search for Unrooted Robinson-Foulds Supertrees

    A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maxim...

    Ruchi Chaudhary, J. Gordon Burleigh… in Bioinformatics Research and Applications (2011)

  5. No Access

    Chapter and Conference Paper

    The Deep Coalescence Consensus Tree Problem is Pareto on Clusters

    Phylogenetic methods must account for the biological processes that create incongruence between gene trees and the species phylogeny. Deep coalescence, or incomplete lineage sorting creates discord among gene ...

    Harris T. Lin, J. Gordon Burleigh… in Bioinformatics Research and Applications (2011)

  6. No Access

    Chapter and Conference Paper

    Algorithms for Rapid Error Correction for the Gene Duplication Problem

    Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within the context of an organismal phylogeny. In one example, the gene duplication problem seeks the evoluti...

    Ruchi Chaudhary, J. Gordon Burleigh… in Bioinformatics Research and Applications (2011)

  7. No Access

    Chapter and Conference Paper

    Locating Multiple Gene Duplications through Reconciled Trees

    We introduce the first exact and efficient algorithm for Guigó et al.’s problem that given a collection of rooted, binary gene trees and a rooted, binary species tree, determines a minimum number of locations ...

    J. Gordon Burleigh, Mukul S. Bansal… in Research in Computational Molecular Biology (2008)

  8. No Access

    Chapter and Conference Paper

    Heuristics for the Gene-Duplication Problem: A Θ(n) Speed-Up for the Local Search

    The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard and thus requires efficient a...

    Mukul S. Bansal, J. Gordon Burleigh… in Research in Computational Molecular Biology (2007)