Unique Perfect Phylogeny Characterizations via Uniquely Representable Chordal Graphs

The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated with the character set, called the partition intersection graph, can be triangulated using a restricted set of fill edges. Semple and Steel used the partition intersection graph to characterize when a character set has a unique perfect phylogeny. Bordewich, Huber, and Semple showed how to use the partition intersection graph to find a maximum compatible set of characters. In this paper, we build on these results, characterizing when a unique perfect phylogeny exists for a subset of partial characters. Our characterization is stated in terms of minimal triangulations of the partition intersection graph that are uniquely representable, also known as ur-chordal graphs. Our characterization is motivated by the structure of ur-chordal graphs, and the fact that the block structure of minimal triangulations is mirrored in the graph that has been triangulated

Simultaneous Graph Representation Problems

Many graphs arising in practice can be represented in a concise and intuitive way that conveys their structure. For example: A planar graph can be represented in the plane with points for vertices and non-crossing curves for edges. An interval graph can be represented on the real line with intervals for vertices and intersection of intervals representing edges. The concept of ``simultaneity'' applies for several types of graphs: the idea is to find representations for two graphs that share some common vertices and edges, and ensure that the common vertices and edges are represented the same way. Simultaneous representation problems arise in any situation where two related graphs should be represented consistently. A main instance is for temporal relationships, where an old graph and a new graph share some common parts. Pairs of related graphs arise in many other situations. For example, two social networks that share some members; two schedules that share some events, overlap graphs of DNA fragments of two similar organisms, circuit graphs of two adjacent layers on a computer chip etc. In this thesis, we study the simultaneous representation problem for several graph classes. For planar graphs the problem is defined as follows. Let G1 and G2 be two graphs sharing some vertices and edges. The simultaneous planar embedding problem asks whether there exist planar embeddings (or drawings) for G1 and G2 such that every vertex shared by the two graphs is mapped to the same point and every shared edge is mapped to the same curve in both embeddings. Over the last few years there has been a lot of work on simultaneous planar embeddings, which have been called `simultaneous embeddings with fixed edges'. A major open question is whether simultaneous planarity for two graphs can be tested in polynomial time. We give a linear-time algorithm for testing the simultaneous planarity of any two graphs that share a 2-connected subgraph. Our algorithm also extends to the case of k planar graphs, where each vertex [edge] is either common to all graphs or belongs to exactly one of them. Next we introduce a new notion of simultaneity for intersection graph classes (interval graphs, chordal graphs etc.) and for comparability graphs. For interval graphs, the problem is defined as follows. Let G1 and G2 be two interval graphs sharing some vertices I and the edges induced by I. G1 and G2 are said to be `simultaneous interval graphs' if there exist interval representations of G1 and G2 such that any vertex of I is assigned to the same interval in both the representations. The `simultaneous representation problem' for interval graphs asks whether G1 and G2 are simultaneous interval graphs. The problem is defined in a similar way for other intersection graph classes. For comparability graphs and any intersection graph class, we show that the simultaneous representation problem for the graph class is equivalent to a graph augmentation problem: given graphs G1 and G2, sharing vertices I and the corresponding induced edges, do there exist edges E' between G1-I and G2-I such that the graph G1 U G_2 U E' belongs to the graph class. This equivalence implies that the simultaneous representation problem is closely related to other well-studied classes in the literature, namely, sandwich graphs and probe graphs. We give efficient algorithms for solving the simultaneous representation problem for interval graphs, chordal graphs, comparability graphs and permutation graphs. Further, our algorithms for comparability and permutation graphs solve a more general version of the problem when there are multiple graphs, any two of which share the same common graph. This version of the problem also generalizes probe graphs

Unique Perfect Phylogeny Characterizations via Uniquely Representable Chordal Graphs

The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated with the character set, called the partition intersection graph, can be triangulated using a restricted set of fill edges. Semple and Steel used the partition intersection graph to characterize when a character set has a unique perfect phylogeny. Bordewich, Huber, and Semple showed how to use the partition intersection graph to find a maximum compatible set of characters. In this paper, we build on these results, characterizing when a unique perfect phylogeny exists for a subset of partial characters. Our characterization is stated in terms of minimal triangulations of the partition intersection graph that are uniquely representable, also known as ur-chordal graphs. Our characterization is motivated by the structure of ur-chordal graphs, and the fact that the block structure of minimal triangulations is mirrored in the graph that has been triangulated

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

Proceedings of the 26th International Symposium on Theoretical Aspects of Computer Science (STACS'09)

The Symposium on Theoretical Aspects of Computer Science (STACS) is held alternately in France and in Germany. The conference of February 26-28, 2009, held in Freiburg, is the 26th in this series. Previous meetings took place in Paris (1984), Saarbr¨ucken (1985), Orsay (1986), Passau (1987), Bordeaux (1988), Paderborn (1989), Rouen (1990), Hamburg (1991), Cachan (1992), W¨urzburg (1993), Caen (1994), M¨unchen (1995), Grenoble (1996), L¨ubeck (1997), Paris (1998), Trier (1999), Lille (2000), Dresden (2001), Antibes (2002), Berlin (2003), Montpellier (2004), Stuttgart (2005), Marseille (2006), Aachen (2007), and Bordeaux (2008). ..