Who is Who in Phylogenetic Networks

Publication no #2086   Type :   Html | Bib | Both

Created: 2011-06-07 15:17:06     Modified: 2011-08-16 11:31:24

2086 Marc Thuillard and Vincent Moulton. Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net. In JBCB, Vol. 9(4):453-470, 2011. Keywords: from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html.         Toggle abstract "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. © 2011 Imperial College Press." @Article{ThuillardMoulton2011,       AUTHOR = {Thuillard, Marc and Moulton, Vincent},       TITLE = {Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net},       YEAR = {2011},       JOURNAL = {JBCB},       VOLUME = {9},       NUMBER = {4},       PAGES = {453-470},       URL = {http://dx.doi.org/10.1142/S0219720011005409},       NOTE = {http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html},       KEYWORDS = {from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction} }