Distinguished minimal topological lassos

The ease with which genomic data can now be generated using Next Generation Sequencing technologies combined with a wealth of legacy data holds great promise for exciting new insights into the evolutionary relationships between and within the kingdoms of life. At the sub-species level (e.g. varieties or strains) certain edge weighted rooted trees with leaf set the set $X$ of organisms under consideration are often used to represent them. Called Dendrograms, it is well-known that they can be uniquely reconstructed from distances provided all distances on $X$ are known. More often than not, real biological datasets do not satisfy this assumption implying that the sought after dendrogram need not be uniquely determined anymore by the available distances with regards to topology, edge-weighting, or both. To better understand the structural properties a set \cL\subseteq {X\choose 2} has to satisfy to overcome this problem, various types of lassos have been introduced. Here, we focus on the question of when a lasso uniquely determines the topology of a dendrogram, that is, it is a topological lasso for it's underlying tree. We show that any set-inclusion minimal topological lasso for such a tree $T$ can be transformed into a structurally nice minimal topological lasso for $T$. Calling such a lasso a distinguished minimal topological lasso for $T$ we characterize them in terms of the novel concept of a cluster marker map for $T$. In addition, we present novel results concerning the heritability of such lassos in the context of the subtree and supertree problems

The square of a block graph

AbstractThe square H2 of a graph H is obtained from H by adding new edges between every two vertices having distance two in H. A block graph is one in which every block is a clique. For the first time, good characterizations and a linear time recognition of squares of block graphs are given in this paper. Our results generalize several previous known results on squares of trees

Clique separator decomposition of hole-free and diamond-free graphs and algorithmic consequences

AbstractClique separator decomposition, introduced by Whitesides and Tarjan, is one of the most important graph decompositions. A hole is a chordless cycle with at least five vertices. A paraglider is a graph with five vertices a,b,c,d,e and edges ab,ac,bc,bd,cd,ae,de. We show that every (hole, paraglider)-free graph admits a clique separator decomposition into graphs of three very specific types. This yields efficient algorithms for various optimization problems in this class of graphs

Graph Powers: Hardness Results, Good Characterizations and Efficient Algorithms

Given a graph H = (V_H,E_H) and a positive integer k, the k-th power of H, written H^k, is the graph obtained from H by adding edges between any pair of vertices at distance at most k in H; formally, H^k = (V_H, {xy | 1 <= d_H (x, y) <= k}). A graph G is the k-th power of a graph H if G = H^k, and in this case, H is a k-th root of G. Our investigations deal with the computational complexity of recognizing k-th powers of general graphs as well as restricted graphs. This work provides new NP-completeness results, good characterizations and efficient algorithms for graph powers

Simplicial Powers of Graphs

In a finite simple undirected graph, a vertex is simplicial if its neighborhood is a clique. We say that, for k ≥ 2, a graph G =(VG,EG) is the k-simplicial power of a graph H =(VH,EH) (H a root graph of G) if VG is the set of all simplicial vertices of H, and for all distinct vertices x and y in VG, xy ∈ EG if and only if the distance in H between x and y is at most k. This concept generalizes k-leaf powers introduced by Nishimura, Ragde and Thilikos which were motivated by the search for underlying phylogenetic trees; k-leaf powers are the k-simplicial powers of trees. Recently, a lot of work has been done on k-leaf powers and their roots as well as on their variants phylogenetic roots and Steiner roots. For k ∈{3, 4, 5}, k-leaf powers can be recognized in linear time, and for k ∈{3, 4}, structural characterizations are known. For all other k, recognition and structural characterization of k-leaf powers is open. Since trees and block graphs (i.e., connected graphs whose blocks are cliques) have very similar metric properties, it is natural to study k-simplicial powers of block graphs. We show that leaf powers of trees and simplicial powers of block graphs are closely related, and we study simplicial powers of other graph classes containing all trees such as ptolemaic graphs and strongly chordal graphs