Results 231 to 240 of about 35,511 (272)

Phylogenomics of sigmodontine rodents (Cricetidae: Sigmodontinae): Cloud forests and Pliocene extinction explain the timing and spread of an iconic South American radiation. [PDF]

PLoS One
Bangs MR, Percequillo AR, Pacheco V, Steppan SJ.   +3 more
europepmc   +1 more source

Deconvolution and phylogeny inference of diverse variant types integrating bulk DNA-seq with single-cell RNA-seq. [PDF]

Bioinform Adv
Bristy NA, Schwartz R.
europepmc   +1 more source

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Sequential Bayesian Phylogenetic Inference

Systematic Biology
Abstract The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost. Instead, phylogenetic pipelines generally consist of sequential analyses, whereby a single point estimate from
Sebastian Höhna, Allison Y Hsiang
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Bayesian phylogenetics

2014
AbstractThis chapter discusses the implementation of various models of genetic sequence evolution in Bayesian phylogenetic analysis. It discusses the specification of priors for parameters in such models, as well as proposals that change those parameters.
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Sequential Bayesian Phylogenetic Inference

2023
Supplementary Material for the manuscript "Sequential Bayesian Phylogenetic Inference"
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Phylogenetic analysis using Bayesian model

Proceedings of the 2014 Zone 1 Conference of the American Society for Engineering Education, 2014
Bayesian inference has been widely applied for phylogenetic and phyloinformatic analysis in recent years. In this paper we build up a high performance computing platform using OpenMPI with free-cost open source Ubuntu Linux operating systems, and then apply the Bayesian inference model to construct a phylogenetic tree of various biological species ...
Wei Lu, Mike Hanrahan
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Parallel algorithms for Bayesian phylogenetic inference

Journal of Parallel and Distributed Computing, 2003
The combination of a Markov chain Monte Carlo (MCMC) method with likelihood-based assessment of phylogenies is becoming a popular alternative to direct likelihood optimization. However, MCMC, like maximum likelihood, is a computationally expensive method. To approximate the posterior distribution of phylogenies, a Markov chain is constructed, using the
Xizhou Feng, Duncan A. Buell, John R. Rose, Peter J. Waddell   +3 more
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Conjugate Gibbs Sampling for Bayesian Phylogenetic Models

Journal of Computational Biology, 2006
We propose a new Markov Chain Monte Carlo (MCMC) sampling mechanism for Bayesian phylogenetic inference. This method, which we call conjugate Gibbs, relies on analytical conjugacy properties, and is based on an alternation between data augmentation and Gibbs sampling.
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Bayesian Phylogenetics with BEAST2

This two-day seminar provides a comprehensive introduction to Bayesian phylogenetics using the powerful BEAST2 software, focusing on building phylogenies and estimating evolutionary dynamics while incorporating prior knowledge and uncertainty. Participants will gain both theoretical understanding and practical skills necessary to conduct sophisticated ...
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Bayesianism, Convergence and Molecular Phylogenetics

2012
Bayesian methods are very popular in molecular phylogenetics. At the same time there is concern among biologists and philosophers regarding the properties of this methodology. In particular, there is concern about the lack of objectivity of evidential statements in Bayesian confirmation theory due to the role of prior probabilities.
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