Related papers: The Complexity of Rooted Phylogeny Problems
The computational complexity of solving random 3-Satisfiability (3-SAT) problems is investigated. 3-SAT is a representative example of hard computational tasks; it consists in knowing whether a set of alpha N randomly drawn logical…
In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…
We prove a complexity dichotomy theorem for a class of Holant problems on planar 3-regular bipartite graphs. The complexity dichotomy states that for every weighted constraint function $f$ defining the problem (the weights can even be…
To answer database queries over incomplete data the gold standard is finding certain answers: those that are true regardless of how incomplete data is interpreted. Such answers can be found efficiently for conjunctive queries and their…
For a first-order theory $T$, the Constraint Satisfaction Problem of $T$ is the computational problem of deciding whether a given conjunction of atomic formulas is satisfiable in some model of $T$. In this article we develop sufficient…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
Trigraph list homomorphism problems (also known as list matrix partition problems) have generated recent interest, partly because there are concrete problems that are not known to be polynomial time solvable or NP-complete. Thus while…
In this paper, we study three algorithmic problems involving computation trees: the optimization, solvability, and satisfiability problems. The solvability problem is concerned with recognizing computation trees that solve problems. The…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
We study the data complexity of consistent query answering (CQA) on databases that may violate the primary key constraints. A repair is a maximal subset of the database satisfying the primary key constraints. For a Boolean query q, the…
Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
This paper categorizes the parameterized complexity of the algorithmic problems Perfect Phylogeny and Triangulating Colored Graphs when parameterized by the number of genes and colors, respectively. We show that they are complete for the…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…