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2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…

In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a properly colored spanning tree, i.e., a spanning tree in which any two adjacent edges have distinct colors. The problem…

The relationship between two important problems in tree pattern matching, the largest common subtree and the smallest common supertree problems, is established by means of simple constructions, which allow one to obtain a largest common…

Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…

Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…

Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…

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…

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…

Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…

Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…

Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…

Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…

Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…

Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…