Related papers: Phylogenetic invariants for $\mathbb{Z}_3$ scheme-…
We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…
Let $\text{Man}_{*}$ denote the category of closed, connected, oriented and based $3$-manifolds, with basepoint preserving diffeomorphisms between them. Juh\'asz, Thurston and Zemke showed that the Heegaard Floer invariants are natural with…
The number of subgroups and the number of cyclic subgroups are natural combinatorial invariants of a finite group. We investigate how restrictions on these quantities, together with the number of distinct prime divisors of $|G|$, enforce…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
It is a recent observation that entanglement classification for qubits is closely related to local $SL(2,\CC)$-invariants including the invariance under qubit permutations, which has been termed $SL^*$ invariance. In order to single out the…
A (discrete) dynamical system may have various symmetries and reversing symmetries, which together form its so-called reversing symmetry group. We study the set of 3D trace maps (obtained from two-letter substitution rules) which preserve…
Congruences, or $2$-parameter families of lines in $3$-space are of interest in many situations, in particular in geometric optics. In this paper we consider elements of their geometry which are invariant under affine changes of…
We consider a conformal invariant of braids, the extremal length with totally real horizontal boundary values $\lambda_{tr}$. The invariant descends to an invariant of elements of $\mathcal{B}_n\diagup\mathcal{Z}_n$, the braid group modulo…
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…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube…
The strand symmetric model is a phylogenetic model designed to reflect the symmetry inherent in the double-stranded structure of DNA. We show that the set of known phylogenetic invariants for the general strand symmetric model of the three…
Let $X$ be a nonempty real variety that is invariant under the action of a reflection group $G$. We conjecture that if $X$ is defined in terms of the first $k$ basic invariants of $G$ (ordered by degree), then $X$ meets a $k$-dimensional…
An (association) scheme is said to be Frobenius if it is the scheme of a Frobenius group. A scheme which has the same tensor of intersection numbers as some Frobenius scheme is said to be pseudofrobenius. We establish a necessary and…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
This series of papers is a contribution to the program of classifying $p$-blocks of finite groups up to source algebra equivalence, starting with the case of cyclic blocks. To any $p$-block $\mathbf{B}$ of a finite group with cyclic defect…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
We give a necessary condition for two diagrams of $3$-regular spatial graphs with the same underlying abstract graph $G$ to represent isotopic spatial graphs. The test works by reading off the writhes of the knot diagrams coming from a…