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Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications. However, sequence data alone often lack enough information to confidently support one gene tree topology over many competing alternatives. Here, we present a novel framework for combining sequence data and species tree information, and we describe(More)
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative(More)
The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped(More)
MOTIVATION Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the(More)
BACKGROUND Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods based on the well established Robinson-Foulds (RF) distance have the potential to build supertrees that retain much information from the input(More)
BACKGROUND Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for processes of gene evolution, such as gene duplication and loss, incomplete lineage sorting (deep coalescence), or horizontal gene transfer,(More)
The NP-hard gene-duplication problem takes as input a collection of gene trees and seeks a species tree that requires the fewest number of gene duplications to reconcile the input gene trees. An oft-cited, decade-old result by Stege states that the gene-duplication problem is fixed parameter tractable when parameterized by the number of gene duplications(More)
The use of genomic data sets for phylogenetics is complicated by the fact that evolutionary processes such as gene duplication and loss, or incomplete lineage sorting (deep coalescence) cause incongruence among gene trees. One well-known approach that deals with this complication is gene tree parsimony, which, given a collection of gene trees, seeks a(More)
UNLABELLED DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In(More)