Related papers: Maximum likelihood estimates of pairwise rearrange…

Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…

We present a unified framework for modelling genomes and their rearrangements in a genome algebra, as elements that simultaneously incorporate all physical symmetries. Building on previous work utilising the group algebra of the symmetric…

The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be…

Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent…

We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…

Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…

We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…

Measuring the distance between two bacterial genomes under the inversion process is usually done by assuming all inversions to occur with equal probability. Recently, an approach to calculating inversion distance using group theory was…

Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…

Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…

A central task in the study of molecular sequence data from present-day species is the reconstruction of the ancestral relationships. The most established approach to tree reconstruction is the maximum likelihood (ML) method. In this…

It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…

Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…

While likelihood-based inference and its variants provide a statistically efficient and widely applicable approach to parametric inference, their application to models involving intractable likelihoods poses challenges. In this work, we…

Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet most reconstruction methods like ML do not explicitly maximize this accuracy. To address this problem, we propose a…