Related papers: Dimensions of Group-based Phylogenetic Mixtures

Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…

Triangular mass matrices for neutrinos and their charged partners contain full information on neutrino mixing in a most concise form. Although the scheme is general and model independent, triangular matrices are typical for reducible but…

Edit distances between merge trees of scalar fields have many applications in scientific visualization, such as ensemble analysis, feature tracking or symmetry detection. In this paper, we propose branch mappings, a novel approach to the…

We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of species post speciation but also allows for species to converge, i.e. become more…

Orthogonal spaces are vector spaces together with a quadratic form whose associated bilinear form is non-degenerate. Over fields of characteristic two, there are many quadratic forms associated to a given bilinear form and quadratic…

The paper is devoted to the study of finite dimensional complex evolution algebras. The class of evolution algebras isomorphic to evolution algebras with Jordan form matrices is described. For finite dimensional complex evolution algebras…

Evolutionary relationships between species are represented by phylogenetic trees, but these relationships are subject to uncertainty due to the random nature of evolution. A geometry for the space of phylogenetic trees is necessary in order…

Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be…

We examine the interplay of symmetry and topological order in $2+1$ dimensional topological phases of matter. We present a definition of the \it topological symmetry \rm group, which characterizes the symmetry of the emergent topological…

The diameter distribution of a given species of deciduous trees in mature, temperate zone forests is well approximated by a Gamma distribution. Here we give new experimental evidence for this conjecture by analyzing deciduous tree size data…

Recent research has established sufficient conditions for finite mixture models to be identifiable from grouped observations. These conditions allow the mixture components to be nonparametric and have substantial (or even total) overlap.…

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…

A noncommutative projective variety is defined, after Artin and Zhang, by a graded coherent algebra A, where the category of coherent sheaves is the quotient qgr(A) of the category of finitely presented graded modules by the subcategory of…

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…

We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…

Phylogenetic invariants are equations that vanish on algebraic varieties associated with Markov processes that model molecular substitutions on phylogenetic trees. For practical applications, it is essential to understand these equations…

Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…

We consider the continuous-time presentation of the strand symmetric phylogenetic substitution model (in which rate parameters are unchanged under nucleotide permutations given by Watson-Crick base conjugation). Algebraic analysis of the…

Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…