Who is Who in Phylogenetic Networks

Publication no #613   Type :   Html | Bib | Both

Created: 2008-03-21 01:22:53     Modified: 2012-08-06 11:44:38

613 Dan Levy and Lior Pachter. The Neighbor-Net Algorithm. In Advances in Applied Mathematics, Vol. 47(2):240-258, 2011. Keywords: abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network. Note: http://arxiv.org/abs/math/0702515.         Toggle abstract "The neighbor-joining algorithm is a popular phylogenetics method for constructing trees from dissimilarity maps. The neighbor-net algorithm is an extension of the neighbor-joining algorithm and is used for constructing split networks. We begin by describing the output of neighbor-net in terms of the tessellation of M̄0n(R) by associahedra. This highlights the fact that neighbor-net outputs a tree in addition to a circular ordering and we explain when the neighbor-net tree is the neighbor-joining tree. A key observation is that the tree constructed in existing implementations of neighbor-net is not a neighbor-joining tree. Next, we show that neighbor-net is a greedy algorithm for finding circular split systems of minimal balanced length. This leads to an interpretation of neighbor-net as a greedy algorithm for the traveling salesman problem. The algorithm is optimal for Kalmanson matrices, from which it follows that neighbor-net is consistent and has optimal radius 12. We also provide a statistical interpretation for the balanced length for a circular split system as the length based on weighted least squares estimates of the splits. We conclude with applications of these results and demonstrate the implications of our theorems for a recently published comparison of Papuan and Austronesian languages. © 2010 Elsevier Inc. All rights reserved." @Article{LevyPachter2008,       AUTHOR = {Levy, Dan and Pachter, Lior},       TITLE = {The Neighbor-Net Algorithm},       YEAR = {2011},       JOURNAL = {Advances in Applied Mathematics},       VOLUME = {47},       NUMBER = {2},       PAGES = {240-258},       URL = {http://dx.doi.org/10.1016/j.aam.2010.09.002},       NOTE = {http://arxiv.org/abs/math/0702515},       ANNOTE = {BIBUPDATE : 20080321},       KEYWORDS = {abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network} }