Who is Who in Phylogenetic Networks

Publications of Sarah Bastkowski     Order by:   Type | Year

Associated keywords

abstract-network circular-split-system from-distances from-quartets heuristic NeighborNet phylogenetic-network phylogeny polynomial Program-FlatNJ Program-QNet Program-SplitsTree Program-SuperQ reconstruction software split-network

Article (Journal)

1 Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute and Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):1057-1058, 2018. Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network. Note: https://doi.org/10.1101/169177.         2 Sarah Bastkowski, Andreas Spillner and Vincent Moulton. Fishing for minimum evolution trees with Neighbor-Nets. In IPL, Vol. 114(1-2):3-18, 2014. Keywords: circular split system, from distances, NeighborNet, phylogeny, polynomial.         Toggle abstract "In evolutionary biology, biologists commonly use a phylogenetic tree to represent the evolutionary history of some set of species. A common approach taken to construct such a tree is to search through the space of all possible phylogenetic trees on the set so as to find one that optimizes some score function, such as the minimum evolution criterion. However, this is hampered by the fact that the space of phylogenetic trees is extremely large in general. Interestingly, an alternative approach, which has received somewhat less attention in the literature, is to instead search for trees within some set of bipartitions or splits of the set of species in question. Here we consider the problem of searching through a set of splits that is circular. Such sets can, for example, be generated by the NeighborNet algorithm for constructing phylogenetic networks. More specifically, we present an O(n4) time algorithm for finding an optimal minimum evolution tree in a circular set of splits on a set of species of size n. In addition, using simulations, we compare the performance of this algorithm when applied to NeighborNet output with that of FastME, a leading method for searching for minimum evolution trees in tree space. We find that, even though a circular set of splits represents just a tiny fraction of the total number of possible splits of a set, the trees obtained from circular sets compare quite favorably with those obtained with FastME, suggesting that the approach could warrant further investigation. © 2013 Elsevier B.V." 3 Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen and Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151-160, 2013. Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.         Toggle abstract "Supertrees are a commonly used tool in phylogenetics to summarize collections of partial phylogenetic trees. As a generalization of supertrees, phylogenetic supernetworks allow, in addition, the visual representation of conflict between the trees that is not possible to observe with a single tree. Here, we introduce SuperQ, a new method for constructing such supernetworks (SuperQ is freely available at >www.uea.ac.uk/computing/superq.). It works by first breaking the input trees into quartet trees, and then stitching these together to form a special kind of phylogenetic network, called a split network. This stitching process is performed using an adaptation of the QNet method for split network reconstruction employing a novel approach to use the branch lengths from the input trees to estimate the branch lengths in the resulting network. Compared with previous supernetwork methods, SuperQ has the advantage of producing a planar network. We compare the performance of SuperQ to the Z-closure and Q-imputation supernetwork methods, and also present an analysis of some published data sets as an illustration of its applicability. © 2004-2012 IEEE."

PhdThesis

4 Sarah Bastkowski. From Trees to Networks and Back. PhD thesis, University of East Anglia, 2013. Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network. Note: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/_downloads/spectre_bastkowskis_thesis.pdf.