相关论文: A tight kernel for computing the tree bisection an…

Tree rearrangement operations typically induce a metric on the space of phylogenetic trees. One important property of these metrics is the size of the neighbourhood, that is, the number of trees exactly one operation from a given tree. We…

Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted…

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…

Rooted phylogenetic networks are rooted acyclic digraphs. They are used to model complex evolution where hybridization, recombination and other reticulation events play important roles. A rigorous definition of network compression is…

The Treewidth-2 Vertex Deletion problem asks whether a set of at most $t$ vertices can be removed from a graph, such that the resulting graph has treewidth at most two. A graph has treewidth at most two if and only if it does not contain a…

The {\sc $k$-Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) with at least $k$ leaves in a given digraph. The problem has recently received much attention from the viewpoint of parameterized…

A branch-and-bound (BB) tree certifies a dual bound on the value of an integer program. In this work, we introduce the tree compression problem (TCP): Given a BB tree T that certifies a dual bound, can we obtain a smaller tree with the same…

The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…

In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…

Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…

The Steiner Tree problem is a classical problem in combinatorial optimization: the goal is to connect a set $T$ of terminals in a graph $G$ by a tree of minimum size. Karpinski and Zelikovsky (1996) studied the $\delta$-dense version of…

Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…

We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…

For an undirected tree with $n$ edges labelled by single letters, we consider its substrings, which are labels of the simple paths between pairs of nodes. We prove that there are $O(n^{1.5})$ different palindromic substrings. This solves an…

Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…

Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…

Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…

We study the CONNECTED \eta-TREEDEPTH DELETION problem where the input instance is an undireted graph G = (V, E) and an integer k. The objective is to decide if G has a set S \subseteq V(G) of at most k vertices such that G - S has…

Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…

Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…