相关论文: Phylogenetic flexibility via Hall-type inequalitie…
We consider the convex hull $P_{\varphi}(G)$ of all satisfying assignments of a given MSO formula $\varphi$ on a given graph $G$. We show that there exists an extended formulation of the polytope $P_{\varphi}(G)$ that can be described by…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
The motivic nearby fiber is an invariant obtained from degenerating a complex variety over a disc. It specializes to the Euler characteristic of the original variety but also contains information on the variation of Hodge structure…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
Suppose we have a set $X$ consisting of $n$ taxa and we are given information from $k$ loci from which to construct a phylogeny for $X$. Each locus offers information for only a fraction of the taxa. The question is whether this data…
Animal and human clusters are complex adaptive systems and many are organized in cluster sizes $s$ that obey the frequency-distribution $D(s)\propto s^{-\tau}$. Exponent $\tau$ describes the relative abundance of the cluster sizes in a…
We prove that a finite dimensional algebra is $\tau$-tilting finite if and only if it does not admit large silting modules. Moreover, we show that for a $\tau$-tilting finite algebra $A$ there is a bijection between isomorphism classes of…
Within the field of phylogenetics there is growing interest in measures for summarising the dissimilarity, or 'incongruence', of two or more phylogenetic trees. Many of these measures are NP-hard to compute and this has stimulated a…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain…
In the representation theory of finite-dimensional algebras, the study of projective presentations of maximal rank is closely related to the study of generically $\tau$-regular irreducible components of varieties of modules over such…
A quasi-hereditary algebra is an algebra equipped with a certain partial order $\unlhd$ on its simple modules. Such a partial order -- called a quasi-hereditary structure -- gives rise to a characteristic tilting module $T_{\unlhd}$ by a…
Tropical rainforests exhibit a rich repertoire of spatial patterns emerging from the intricate relationship between the microscopic interaction between species. In particular, the distribution of vegetation clusters can shed much light on…