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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...
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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...
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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...
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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 ...
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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...