Results 11 to 20 of about 31,734 (247)
Adaptive Tree Proposals for Bayesian Phylogenetic Inference. [PDF]
Syst Biol, 2021 Abstract Bayesian inference of phylogenies with MCMC is without a doubt a staple in the study of evolution. Yet, this method still suffers from a practical challenge identified more than two decades ago: designing tree topology proposals that efficiently sample the tree space.
Meyer X.
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Bayesian inference of phylogenetic networks from bi-allelic genetic markers.
PLoS Computational Biology, 2018 Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple ...
Jiafan Zhu +4 more
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FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods [PDF]
BMC Bioinformatics, 2010 Background Likelihood (ML)-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data.
Bakos Jason D, Zierke Stephanie
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Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent. [PDF]
Mol Biol Evol, 2022 Abstract The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes–Cantor model, and ...
Flouri T +5 more
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On the importance of assessing topological convergence in Bayesian phylogenetic inference. [PDF]
Virus EvolAbstract Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples.
Brusselmans M +9 more
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An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference [PDF]
Systematic Biology, 2021 Abstract We present a two headed approach called Bayesian Integrated Coalescent Epoch PlotS (BICEPS) for efficient inference of coalescent epoch models. Firstly, we integrate out population size parameters and secondly we introduce a set of more powerful Markov chain Monte Carlo (MCMC) proposals for flexing and stretching trees.
Bouckaert RR.
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Particle Gibbs sampling for Bayesian phylogenetic inference [PDF]
Bioinformatics, 2020 Abstract Motivation The combinatorial sequential Monte Carlo (CSMC) has been demonstrated to be an efficient complementary method to the standard Markov chain Monte Carlo (MCMC) for Bayesian phylogenetic tree inference using biological sequences.
Shijia Wang, Liangliang Wang 0002
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A Variational Approach to Bayesian Phylogenetic Inference
CoRR, 2022 Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper, we present an alternative approach: a variational framework for Bayesian phylogenetic analysis.
Cheng Zhang, Frederick A. Matsen IV
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Polytomies and Bayesian Phylogenetic Inference [PDF]
Systematic Biology, 2005 Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths ...
Lewis, Paul O +2 more
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Three novel species of Helminthosporium (Massarinaceae, Pleosporales) from China [PDF]
MycoKeys, 2022 Three new species of Helminthosporium, H. nabanhensis, H. sinensis and H. yunnanensis collected on dead branches of unidentified plants in Xishuangbanna, China, were proposed by morphological and molecular phylogenetic analysis.
Jingwen Liu +4 more
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