相关论文: Quantifying the accuracy of ancestral state predic…

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…

Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…

We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…

For different reversible Markov kernels on finite state spaces, we look for families of probability measures for which the time evolution almost remains in their convex hull. Motivated by signal processing problems and metastability studies…

A central task in the study of molecular sequence data from present-day species is the reconstruction of the ancestral relationships. The most established approach to tree reconstruction is the maximum likelihood (ML) method. In this…

We consider a broadcasting problem on a tree where a binary digit (e.g., a spin or a nucleotide's purine/pyrimidine type) is propagated from the root to the leaves through symmetric noisy channels on the edges that randomly flip the state…

Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…

Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…

We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…

In this article we prove that the distance $d_{\mathrm{MP}}(T_1,T_2) = k$ between two unrooted binary phylogenetic trees $T_1, T_2$ on the same set of taxa can be defined by a character that is convex on one of $T_1, T_2$ and which has at…

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…

We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…

We investigate the evolutionary dynamics of a population structured in phenotype, subjected to trait dependent selection with a linearly moving optimum and an asexual mode of reproduction. Our model consists of a non-local and non-linear…

Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to converge to the true value in the independent-sample case, we…

The reconstruction of phylogenetic trees from discrete character data typically relies on models that assume the characters evolve under a continuous-time Markov process operating at some overall rate $\lambda$. When $\lambda$ is too high…

Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…

Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…

We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each…