Related papers: Cophylogeny Reconstruction Allowing for Multiple A…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Faithful generation in large language models (LLMs) is challenged by knowledge conflicts between parametric memory and external context. Existing contrastive decoding methods tuned specifically to handle conflict often lack adaptability and…
We study and compare fitting methods for the Lyman-$\alpha$ (Ly$\alpha$) forest 3D correlation function. We use the nested sampler PolyChord and the community code picca to perform a Bayesian analysis which we compare with previous…
The tree is an essential data structure in many applications. In a distributed application, such as a distributed file system, the tree is replicated.To improve performance and availability, different clients should be able to update their…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single…
Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits…
Previously, we presented PanelPRO, now known as Fam3PRO, an open-source R package for multi-gene, multi-cancer risk modeling with pedigree data. The initial release could not handle pedigrees that contained cyclic structures called loops,…
Recombining trinomial trees are a workhorse for modeling discrete-event systems in option pricing, logistics, and feedback control. Because each node stores a state-dependent quantity, a depth-$D$ tree naively yields $\mathcal{O}(3^{D})$…
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…
BPEC is an R package for Bayesian Phylogeographic and Ecological Clustering which allows geographical, environmental and phenotypic measurements to be combined with DNA sequences in order to reveal clustered structure resulting from…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
ASTRAL is a method for reconstructing species trees after inferring a set of gene trees and is increasingly used in phylogenomic analyses. It is statistically consistent under the multi-species coalescent model, is scalable, and has shown…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
We introduce a simple and extendable coevolution model for the analysis of longitudinal network and nodal attribute data. The model features parameters that describe three phenomena: homophily, contagion and autocorrelation of the network…
In recent years, the explosion of malware and extensive code reuse have formed complex evolutionary connections among malware specimens. The rapid pace of development makes it challenging for existing studies to characterize recent…