Who is Who in Phylogenetic Networks

Publications of Paul Phipps     Order by:   Type | Year

Associated keywords

abstract-network from-distances from-splits phylogenetic-network phylogeny Program-PhippsNetwork reconstruction software split split-network

Article (Journal)

1 Paul Phipps and Sergey Bereg. Optimizing Phylogenetic Networks for Circular Split Systems. In TCBB, Vol. 9(2):535-547, 2012. Keywords: abstract network, from distances, from splits, phylogenetic network, phylogeny, Program PhippsNetwork, reconstruction, software.         Toggle abstract "We address the problem of realizing a given distance matrix by a planar phylogenetic network with a minimum number of faces. With the help of the popular software SplitsTree4, we start by approximating the distance matrix with a distance metric that is a linear combination of circular splits. The main results of this paper are the necessary and sufficient conditions for the existence of a network with a single face. We show how such a network can be constructed, and we present a heuristic for constructing a network with few faces using the first algorithm as the base case. Experimental results on biological data show that this heuristic algorithm can produce phylogenetic networks with far fewer faces than the ones computed by SplitsTree4, without affecting the approximation of the distance matrix. © 2012 IEEE."

PhdThesis

2 Paul Phipps. Planar phylogenetic network optimization. PhD thesis, University of Texas at Dallas, U.S.A., 2011. Keywords: abstract network, from distances, phylogenetic network, Program PhippsNetwork, split, split network. Note: http://proquest.umi.com/pqdlink?did=2337197411&Fmt=7&clientId=176295&RQT=309&VName=PQD.