10 citations · 12 across the 6 of their papers we have counts for
8 papers · 1 filter
Assessing the Validity of the Fixed Tree Topology Assumption in Phylodynamic Inference
Mathieu Fourment, Jiansi Gao, Marc A Suchard +1
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we sy…
Generalizing matrix representations to fully heterochronous ranked tree shapes
Chris Jennings-Shaffer, Ziyue, Chen +2
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible wit…
Torchtree: flexible phylogenetic model development and inference using PyTorch
Mathieu Fourment, Matthew Macaulay, Christiaan J Swanepoel +3
Bayesian inference has predominantly relied on the Markov chain Monte Carlo (MCMC) algorithm for many years. However, MCMC is computationally laborious, especially for complex phyl…
On the importance of assessing topological convergence in Bayesian phylogenetic inference
Marius Brusselmans, Luiz Max Carvalho, Samuel L. Hong +7
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distrib…
The structure of deviations from maximum parsimony for densely-sampled data and applications for clade support estimation
William Howard-Snyder, Will Dumm, Mary Barker +5
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the…
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
Will Dumm, Mary Barker, William Howard-Snyder +2
In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed…
Online Bayesian phylogenetic inference: theoretical foundations via Sequential Monte Carlo
Vu Dinh, Aaron E. Darling, Frederick A. Matsen
Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological sys…
A method for investigating relative timing information on phylogenetic trees
Daniel Ford, Tanja Gernhard, Frederick Matsen
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events…