BEAST

swMATH12588MaRDI QIDQ24514FDOQ24514

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Official website: http://beast2.org/

Described by source

• Bayesian evolutionary analysis with BEAST

Cited In (71)

• Batch Matrix Exponentiation
• A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses
• Genetic demographic networks: mathematical model and applications
• An adjacent-swap Markov chain on coalescent trees
• Fitting stochastic epidemic models to gene genealogies using linear noise approximation
• Comment on article by Rubio and Steel
• Combinatorial perspectives on Dollo-\(k\) characters in phylogenetics
• On incomplete sampling under birth-death models and connections to the sampling-based coalescent
• Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph
• A representation-theoretic approach to the calculation of evolutionary distance in bacteria
• Inferring contagion patterns in social contact networks with limited infection data
• Exact and approximate limit behaviour of the Yule tree's cophenetic index
• The coalescence of intrahost HIV lineages under symmetric CTL attack
• Geometric ergodicity of a Metropolis-Hastings algorithm for Bayesian inference of phylogenetic branch lengths
• Efficient Bayesian inference of general Gaussian models on large phylogenetic trees
• Objective Bayesian analysis for Gaussian hierarchical models with intrinsic conditional autoregressive priors
• Modeling sequence evolution in HIV-1 infection with recombination
• Demographic inference under the coalescent in a spatial continuum
• Sequential Monte Carlo with transformations
• Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
• Enumeration of binary trees compatible with a perfect phylogeny
• Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
• Stochastic epidemic models inference and diagnosis with Poisson random measure data augmentation
• A semiparametric Bayesian approach to epidemics, with application to the spread of the coronavirus MERS in South Korea in 2015
• Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks
• Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: theory and applications
• The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes
• Statistical challenges in tracking the evolution of SARS-CoV-2
• Developments in coalescent theory from single loci to chromosomes
• Sequential importance sampling for multiresolution Kingman-Tajima coalescent counting
• The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events
• Adaptive Preferential Sampling in Phylodynamics With an Application to SARS-CoV-2
• Sampling-through-time in birth-death trees
• Sampling HIV intrahost genealogies based on a model of acute stage CTL response
• Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies
• ape
• Representations of partial leaf sets in phylogenetic tree space
• Partition Weighted Approach For Estimating the Marginal Posterior Density With Applications
• Phylogenetic network dissimilarity measures that take branch lengths into account
• MEGA
• rSPR
• Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths
• Protein domain hierarchy Gibbs sampling strategies
• DensiTree
• Partitionfinder
• spr_neighbors
• phyloTop
• FastTree
• ccaPP
• Visualizing codon usage within and across genomes: concepts and tools
• Modeling sequence evolution in acute HIV-1 infection
• Exact limits of inference in coalescent models
• Computing nearest neighbour interchange distances between ranked phylogenetic trees
• Finding outbreak trees in networks with limited information
• Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret
• Consistency and identifiability of the polymorphism-aware phylogenetic models
• Bayesian-weighted triplet and quartet methods for species tree inference
• Discrete coalescent trees
• The space of ultrametric phylogenetic trees
• Slicing and dicing the genome: A statistical physics approach to population genetics
• Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
• Uncertainty in Phylogenetic Tree Estimates
• Coalescent models derived from birth-death processes
• Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
• Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies
• Calculations for multi-type age-dependent binary branching processes
• An extended model for phylogenetic maximum likelihood based on discrete morphological characters
• TruncatedNormal
• Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees
• Efficiently inferring pairwise subtree prune-and-regraft adjacencies between phylogenetic trees
• Consistency of a phylogenetic tree maximum likelihood estimator

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