相关论文: Efficient FPT algorithms for (strict) compatibilit…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…

Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced…

Phylogenetic networks allow modeling reticulate evolution, capturing events such as hybridization and horizontal gene transfer. A fundamental computational problem in this context is the Tree Containment problem, which asks whether a given…

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

In the NP-hard Optimizing PD with Dependencies (PDD) problem, the input consists of a phylogenetic tree $T$ over a set of taxa $X$, a food-web that describes the prey-predator relationships in $X$, and integers $k$ and $D$. The task is to…

We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…

Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…

A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…

The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…

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…

Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…

The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…

Within the field of phylogenetics there is growing interest in measures for summarising the dissimilarity, or 'incongruence', of two or more phylogenetic trees. Many of these measures are NP-hard to compute and this has stimulated a…

In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…

One of the important features of an interconnection network is its ability to efficiently simulate programs or parallel algorithms written for other architectures. Such a simulation problem can be mathematically formulated as a graph…