Related papers: Phylogenetic invariants for $\mathbb{Z}_3$ scheme-…
The goal of invariant theory is to find all the generators for the algebra of representations of a group that leave the group invariant. Such generators will be called \emph{basic invariants}. In particular, we set out to find the set of…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
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…
Let $\mathcal{G}$ denote the variety generated by infinite dimensional Grassmann algebras; i.e., the collection of all unitary associative algebras satisfying the identity $[[z_1,z_2],z_3]=0$, where $[z_i,z_j]=z_iz_j-z_jz_i$. Consider the…
Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…
The space of n (ordered) points on the projective line, modulo automorphisms of the line, is one of the most important and classical examples of an invariant theory quotient, and is one of the first examples given in any course. Generators…
Many finite groups, including all finite non-abelian simple groups, can be symmetrically generated by involutions. In this paper we give an algorithm to symmetrically represent elements of finite groups and to transform symmetrically…
We consider a projective transformation and establish the invariants for this transformation group up to order seven. We use the obtained invariants to construct a class of nonlinear evolution equations and identify some symmetry-integrable…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…
We consider evolution equations for curves in the 3-dimensional sphere $S^3$ that are invariant under the group $SU(2,1)$ of pseudoconformal transformations, which preserves the standard contact structure on the sphere. In particular, we…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
We provide a complete classification of normal phylogenetic varieties coming from tripods, and more generally, from trivalent trees. Let $G$ be an abelian group. We prove that the group-based phylogenetic variety $X_{G,\mathcal{T}}$, for…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
Recent classification of $\frac{3}{2}$-transitive permutation groups leaves us with six families of groups which are $2$-transitive, or Frobenius, or one-dimensional affine, or the affine solvable subgroups of $ \mathrm{AGL}(2, q)$, or…
In this paper, we establish a bijection between the set of mutation classes of mutation-cyclic skew-symmetric integral 3x3-matrices and the set of triples of integers (a,b,c) which are all greater than 1 and where the product of the two…
The algebra of invariants of d-tuples of n x n skew-symmetric matrices under the action of the orthogonal group by simultaneous conjugation is considered over an infinite field of characteristic different from two. For n=3 and d>0 a minimal…
Recent classification of $\frac{3}{2}$-transitive permutation groups leaves us with three infinite families of groups which are neither $2$-transitive, nor Frobenius, nor one-dimensional affine. The groups of the first two families…
We discuss the isomorphism problem of projective schemes; given two projective schemes, can we algorithmically decide whether they are isomorphic? We give affirmative answers in the case of one-dimensional projective schemes, the case of…
We study the relationship between two notions of pattern avoidance for involutions in the symmetric group and their restriction to fixed-point-free involutions. The first is classical, while the second appears in the geometry of certain…