Cited in
(only showing first 100 items - show all)- hdtg
- Sampling-through-time in birth-death trees
- Adaptive Preferential Sampling in Phylodynamics With an Application to SARS-CoV-2
- Sampling HIV intrahost genealogies based on a model of acute stage CTL response
- RAxML-NG
- Phylogenetic network dissimilarity measures that take branch lengths into account
- Partition Weighted Approach For Estimating the Marginal Posterior Density With Applications
- Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies
- Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths
- Representations of partial leaf sets in phylogenetic tree space
- Protein domain hierarchy Gibbs sampling strategies
- Modeling sequence evolution in acute HIV-1 infection
- Exact limits of inference in coalescent models
- Visualizing codon usage within and across genomes: concepts and tools
- 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
- An adjacent-swap Markov chain on coalescent trees
- Slicing and dicing the genome: A statistical physics approach to population genetics
- adapref
- SurvGPR
- Fitting stochastic epidemic models to gene genealogies using linear noise approximation
- Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
- Coalescent models derived from birth-death processes
- Uncertainty in Phylogenetic Tree Estimates
- Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
- SpaceMix
- Calculations for multi-type age-dependent binary branching processes
- Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies
- An extended model for phylogenetic maximum likelihood based on discrete morphological characters
- Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees
- Efficiently inferring pairwise subtree prune-and-regraft adjacencies between phylogenetic trees
- Combinatorial perspectives on Dollo-\(k\) characters in phylogenetics
- Consistency of a phylogenetic tree maximum likelihood estimator
- Comment on article by Rubio and Steel
- 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
- Inferring contagion patterns in social contact networks with limited infection data
- A representation-theoretic approach to the calculation of evolutionary distance in bacteria
- 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
- Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
- Demographic inference under the coalescent in a spatial continuum
- Sequential Monte Carlo with transformations
- Enumeration of binary trees compatible with a perfect phylogeny
- Stochastic epidemic models inference and diagnosis with Poisson random measure data augmentation
- Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
- Batch Matrix Exponentiation
- 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
- A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses
- 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
- Genetic demographic networks: mathematical model and applications
- ape
- fastDNAml
- MrBayes
- RAxML
- PAUP*
- phangorn
- Seq-Gen
- MEGA
- PhyML
- Arlequin
- LAMARC
- simuPOP
- BEAGLE
- BEAUti
- DPRml
- pIQPNNI
- GPUTeraSort
- rSPR
- BioWar
- SPRSupertrees
- rwty
- Bali-phy
- IQ-TREE
- NINJA
- Phylo-MCOA
- TNT
- phylodyn
- ASTRAL-II
- kdetrees
- TOPD/FMTS
- PhyloNet
- Dendroscope
- ACEMD
- DensiTree
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