Related papers: Fast error-tolerant quartet phylogeny algorithms
Control and characterization of networks is a paramount step for the development of many quantum technologies. Even for moderate-sized networks, this amounts to explore an extremely vast parameters space in search for the couplings defining…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We present a family of algorithms, combining real-space renormalization methods and belief propagation, to estimate the free energy of a topologically ordered system in the presence of defects. Such an algorithm is needed to preserve the…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
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 reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
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…
The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet which tries to construct an optimal rooted phylogenetic…
We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
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…
Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for…
Given a set of n data objects and their pairwise dissimilarities, the goal of the minimum quartet tree cost (MQTC) problem is to construct an optimal tree from the total number of possible combinations of quartet topologies on n, where…
We present an algorithm that, with high probability, generates a random spanning tree from an edge-weighted undirected graph in $\tilde{O}(n^{4/3}m^{1/2}+n^{2})$ time (The $\tilde{O}(\cdot)$ notation hides $\operatorname{polylog}(n)$…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
We present an efficient and flexible method for computing likelihoods of phenotypic traits on a phylogeny. The method does not resort to Monte-Carlo computation but instead blends Felsenstein's discrete character pruning algorithm with…