Related papers: Quartet consistency count method for reconstructin…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
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…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
In this paper we design and prove correct a fully dynamic distributed algorithm for maintaining an approximate Steiner tree that connects via a minimum-weight spanning tree a subset of nodes of a network (referred as Steiner members or…
We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…
Nearest neighbor (kNN) methods have been gaining popularity in recent years in light of advances in hardware and efficiency of algorithms. There is a plethora of methods to choose from today, each with their own advantages and…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all displayed quartets in many practical problems due to the…
Embeddings of graphs into distributions of trees that preserve distances in expectation are a cornerstone of many optimization algorithms. Unfortunately, online or dynamic algorithms which use these embeddings seem inherently randomized and…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…