Fidelity of hyperbolic space for Bayesian phylogenetic inference. [PDF]
PLoS Computational Biology, 2023 Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. However, Bayesian phylogenetics faces the challenging computational problem of moving throughout the high-dimensional space of trees.
Matthew Macaulay +2 more
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Early cephalopod evolution clarified through Bayesian phylogenetic inference [PDF]
BMC Biology, 2022 Background Despite the excellent fossil record of cephalopods, their early evolution is poorly understood. Different, partly incompatible phylogenetic hypotheses have been proposed in the past, which reflected individual author’s opinions on the ...
Alexander Pohle +8 more
doaj +2 more sources
Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) [version 3; peer review: 3 approved, 1 approved with reservations] [PDF]
Open Research Europe, 2023 Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of ...
Orlando Schwery +4 more
doaj +2 more sources
Improving the performance of Bayesian phylogenetic inference under relaxed clock models [PDF]
BMC Evolutionary Biology, 2020 Background Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms ...
Rong Zhang, Alexei Drummond
doaj +2 more sources
Bayesian inference of mixed Gaussian phylogenetic models [PDF]
BMC BioinformaticsBackground Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of traits through time, while ...
Bayu Brahmantio +2 more
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Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings. [PDF]
PLoS Computational BiologyMulticellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking
Julia Pilarski +2 more
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Bayesian phylogenetic inference of HIV latent lineage ages using serial sequences [PDF]
Journal of the Royal Society Interface, 2023 Bruce Rannala, Anna Nagel
exaly +2 more sources
Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo [PDF]
Systematic Biology, 2018 Frederick Matsen +2 more
exaly +2 more sources
Molecular timetrees using relaxed clocks and uncertain phylogenies
Frontiers in Bioinformatics, 2023 A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and
Jose Barba-Montoya +5 more
doaj +1 more source
Open Research Europe, 2023 Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of ...
Orlando Schwery +4 more
doaj +1 more source