Related papers: Using the tangle: a consistent construction of phy…
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
Discovering the latent structure from many observed variables is an important yet challenging learning task. Existing approaches for discovering latent structures often require the unknown number of hidden states as an input. In this paper,…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
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…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Although recovering an Euclidean distance matrix from noisy observations is a common problem in practice, how well this could be done remains largely unknown. To fill in this void, we study a simple distance matrix estimate based upon the…
This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
The matching distance is a computationally tractable topological measure to compare multi-filtered simplicial complexes. We design efficient algorithms for approximating the matching distance of two bi-filtered complexes to any desired…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of 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…
The neighbor-joining algorithm is a popular phylogenetics method for constructing trees from dissimilarity maps. The neighbor-net algorithm is an extension of the neighbor-joining algorithm and is used for constructing split networks. We…