Who is Who in Phylogenetic Networks

Publications of Kunihiko Sadakane     Order by:   Type | Year

Associated keywords

distance-between-networks dynamic-programming explicit-network FPT from-rooted-trees k-reticulated level-k-phylogenetic-network MASN NP-complete phylogenetic-network phylogeny polynomial Program-ARTNET Program-CMPT reconstruction spread

Article (Journal)

1 Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster computation of the Robinson–Foulds distance between phylogenetic networks. In Information Sciences, Vol. 197:77-90, 2012. Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.         Toggle abstract "The Robinson-Foulds distance, a widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two phylogenetic networks N 1, N 2 with n leaf labels and at most m nodes and e edges each, the Robinson-Foulds distance measures the number of clusters of descendant leaves not shared by N 1 and N 2. The fastest known algorithm for computing the Robinson-Foulds distance between N 1 and N 2 runs in O(me) time. In this paper, we improve the time complexity to O(ne/log n) for general phylogenetic networks and O(nm/log n) for general phylogenetic networks with bounded degree (assuming the word RAM model with a word length of ⌈logn⌉ bits), and to optimal O(m) time for leaf-outerplanar networks as well as optimal O(n) time for level-1 phylogenetic networks (that is, galled-trees). We also introduce the natural concept of the minimum spread of a phylogenetic network and show how the running time of our new algorithm depends on this parameter. As an example, we prove that the minimum spread of a level-k network is at most k + 1, which implies that for one level-1 and one level-k phylogenetic network, our algorithm runs in O((k + 1)e) time. © 2012 Elsevier Inc. All rights reserved." 2 Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In TCS, Vol. 335(1):93-107, 2005. Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny. Note: http://www.df.lth.se/~jj/Publications/masn8_TCS2005.pdf.         Toggle abstract "We introduce the maximum agreement phylogenetic subnetwork problem (MASN) for finding branching structure shared by a set of phylogenetic networks. We prove that the problem is NP-hard even if restricted to three phylogenetic networks and give an O(n2)-time algorithm for the special case of two level-1 phylogenetic networks, where n is the number of leaves in the input networks and where N is called a level-f phylogenetic network if every biconnected component in the underlying undirected graph induces a subgraph of N containing at most f nodes with indegree 2. We also show how to extend our technique to yield a polynomial-time algorithm for any two level-f phylogenetic networks N1,N2 satisfying f=O(logn); more precisely, its running time is O(|V(N1)|·|V(N2)|·2f1+f2), where V(Ni) and fi denote the set of nodes in Ni and the level of Ni, respectively, for i∈{1,2}. © 2005 Elsevier B.V. All rights reserved."

InProceedings

3 Hoa Vu, Francis Chin, Wing-Kai Hon, Henry Leung, Kunihiko Sadakane, Wing-Kin Sung and Siu-Ming Yiu. Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees. In ISBRA13, Vol. 7875:112-124 of LNCS, springer, 2013. Keywords: from rooted trees, k-reticulated, phylogenetic network, phylogeny, polynomial, Program ARTNET, Program CMPT, reconstruction. Note: http://grid.cs.gsu.edu/~xguo9/publications/2013_Cloud%20computing%20for%20de%20novo%20metagenomic%20sequence%20assembly.pdf#page=123.         Toggle abstract "The time complexity of existing algorithms for reconstructing a level-x phylogenetic network increases exponentially in x. In this paper, we propose a new classification of phylogenetic networks called k-reticulated network. A k-reticulated network can model all level-k networks and some level-x networks with x > k. We design algorithms for reconstructing k-reticulated network (k = 1 or 2) with minimum number of hybrid nodes from a set of m binary trees, each with n leaves in O(mn 2) time. The implication is that some level-x networks with x > k can now be reconstructed in a faster way. We implemented our algorithm (ARTNET) and compared it with CMPT. We show that ARTNET outperforms CMPT in terms of running time and accuracy. We also consider the case when there does not exist a 2-reticulated network for the input trees. We present an algorithm computing a maximum subset of the species set so that a new set of subtrees can be combined into a 2-reticulated network. © 2013 Springer-Verlag." 4 Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190-201 of LNCS, springer, 2010. Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread. Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.         Toggle abstract "The Robinson-Foulds distance, which is the most widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two networks N1,N2 with n leaves, m nodes, and e edges, the Robinson-Foulds distance measures the number of clusters of descendant leaves that are not shared by N1 and N2. The fastest known algorithm for computing the Robinson-Foulds distance between those networks runs in O(m(m + e)) time. In this paper, we improve the time complexity to O(n(m+ e)/ log n) for general networks and O(nm/log n) for general networks with bounded degree, and to optimal O(m + e) time for planar phylogenetic networks and boundedlevel phylogenetic networks.We also introduce the natural concept of the minimum spread of a phylogenetic network and show how the running time of our new algorithm depends on this parameter. As an example, we prove that the minimum spread of a level-k phylogenetic network is at most k + 1, which implies that for two level-k phylogenetic networks, our algorithm runs in O((k + 1)(m + e)) time. © Springer-Verlag Berlin Heidelberg 2010." 5 Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS'04), Vol. 91:134-147 of Electronic Notes in Theoretical Computer Science, 2004. Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny. Note: http://www.df.lth.se/~jj/Publications/masn6_CATS2004.pdf.         Toggle abstract "We introduce the maximum agreement phylogenetic subnetwork problem (MASN) of finding a branching structure shared by a set of phylogenetic networks. We prove that the problem is NP-hard even if restricted to three phylogenetic networks and give an O(n2)-time algorithm for the special case of two level-1 phylogenetic networks, where n is the number of leaves in the input networks and where N is called a level-f phylogenetic network if every biconnected component in the underlying undirected graph contains at most f nodes having indegree 2 in N. Our algorithm can be extended to yield a polynomial-time algorithm for two level-f phylogenetic networks N 1,N2 for any f which is upper-bounded by a constant; more precisely, its running time is O(|V(N1)|·|V(N 2)|·4f), where V(Ni) denotes the set of nodes of Ni. © 2004 Published by Elsevier B.V."