{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T13:07:46Z","timestamp":1648904866094},"reference-count":33,"publisher":"World Scientific Pub Co Pte Lt","issue":"04","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2011,8]]},"abstract":"<jats:p> Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota. <\/jats:p>","DOI":"10.1142\/s0219720011005409","type":"journal-article","created":{"date-parts":[[2011,3,8]],"date-time":"2011-03-08T11:23:27Z","timestamp":1299583407000},"page":"453-470","source":"Crossref","is-referenced-by-count":4,"title":["IDENTIFYING AND RECONSTRUCTING LATERAL TRANSFERS FROM DISTANCE MATRICES BY COMBINING THE MINIMUM CONTRADICTION METHOD AND NEIGHBOR-NET"],"prefix":"10.1142","volume":"09","author":[{"given":"MARC","family":"THUILLARD","sequence":"first","affiliation":[{"name":"La Colline, Creuze 9, CH-2072 St-Blaise, Switzerland"}]},{"given":"VINCENT","family":"MOULTON","sequence":"additional","affiliation":[{"name":"School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","first-page":"90","volume":"2","author":"Doolittle W. 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