Related papers: A Corrected Parsimony Criterion for Reconstructing…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
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…
The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for…
Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be…
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
Tuffley and Steel (1997) proved that Maximum Likelihood and Maximum Parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
Finding optimal evolutionary trees from sequence data is typically an intractable problem, and there is usually no way of knowing how close to optimal the best tree from some search truly is. The problem would seem to be particularly acute…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Phylogenetic approaches to classification have been heavily developed in biology by bioinformaticians. But these techniques have applications in other fields, in particular in linguistics. Their main characteristics is to search for…