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We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families. The gene duplication and loss process is a major cause for incongruence between gene and species tree, and deterministic methods have been developed to explain such(More)
The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene(More)
MOTIVATION The identification of regulatory control regions within genomes is a major challenge. Studies have demonstrated that regulating regions can be described as locally dense clusters or modules of cis-acting transcription factor binding sites (TFBS). For well-described biological contexts, it is possible to train predictive algorithms to discern(More)
Gene tree and species tree reconstruction, orthology analysis and reconciliation, are problems important in multigenome-based comparative genomics and biology in general. In the present paper, we advance the frontier of these areas in several respects and provide important computational tools. First, exact algorithms are given for several probabilistic(More)
R c 1997 The Massachusetts Institute of Technology. Subscribers are licensed to use journal articles in a variety of ways, limited only as required to insure fair attribution to authors and the journal, and to prohibit use in a competing commercial product. See the journal's World Wide Web site for further details. The Chicago Journal of Theoretical(More)
A collection of T 1 , T 2 ,. .. , T k of unrooted, leaf labelled (phylogenetic) trees, all with different leaf sets, is said to be compatible if there exists a tree T such that each tree T i can be obtained from T by deleting leaves and contracting edges. Determining compatibility is NP-hard, and the fastest algorithm to date has worst case complexity of(More)
Identification of functional transcription factor binding sites in genomic sequences is notoriously difficult. The critical problem is the low specificity of predictions, which directly reflects the low target specificity of DNA binding proteins. To overcome the noise produced in predictions of individual binding sites, a new generation of algorithms(More)
SUMMARY PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species.(More)