Related papers: Revisiting an equivalence between maximum parsimon…
In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex $v$ of an evolutionary tree $T$ from the states that are observed at the leaves of the tree. A simple and fast…
Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…
Maximum likelihood estimation (MLE) methods are widely used for evolutionary tree. As evolutionary tree is not a smooth parameter, the consistency of its MLE has been a topic of debate. It has been noted without proof that the classical…
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…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the…
Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
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)…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
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…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
We address the problem of data clustering by introducing an unsupervised, parameter free approach based on maximum likelihood principle. Starting from the observation that data sets belonging to the same cluster share a common information,…
Can autoregressive large language models (LLMs) learn consistent probability distributions when trained on sequences in different token orders? We prove formally that for any well-defined probability distribution, sequence perplexity is…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…