On unrooted and root-uncertain variants of several well-known phylogenetic network problems

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.Comment: 28 pages, 8 Figure

Random Boolean Networks

This review explains in a self-contained way the properties of random Boolean networks and their attractors, with a special focus on critical networks. Using small example networks, analytical calculations, phenomenological arguments, and problems to solve, the basic concepts are introduced and important results concerning phase diagrams, numbers of relevant nodes and attractor properties are derived.Comment: This is a review on Random Boolean Networks. The new version now includes a proper title page. The main body is unchange

Max flow vitality in general and stst-planar graphs

The \emph{vitality} of an arc/node of a graph with respect to the maximum flow between two fixed nodes $s$ and $t$ is defined as the reduction of the maximum flow caused by the removal of that arc/node. In this paper we address the issue of determining the vitality of arcs and/or nodes for the maximum flow problem. We show how to compute the vitality of all arcs in a general undirected graph by solving only $2(n-1)$ max flow instances and, In $st$-planar graphs (directed or undirected) we show how to compute the vitality of all arcs and all nodes in $O(n)$ worst-case time. Moreover, after determining the vitality of arcs and/or nodes, and given a planar embedding of the graph, we can determine the vitality of a `contiguous' set of arcs/nodes in time proportional to the size of the set.Comment: 12 pages, 3 figure