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The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Systematic Biology
, 2014
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which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
The theta correspondence and
"... Identification and functional characterization of NifA variants that are independent of GlnB activation in the photosynthetic bacterium Rhodospirillum rubrum ..."
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Identification and functional characterization of NifA variants that are independent of GlnB activation in the photosynthetic bacterium Rhodospirillum rubrum
2013 IEEE 27th International Symposium on Parallel & Distributed Processing Workshops and PhD Forum Boosting the performance of Bayesian divergence time estimation with the Phylogenetic Likelihood Library
"... Abstract—We present a substantially improved and parallelized version of DPPDiv, a software tool for estimating species divergence times and lineagespecific substitution rates on a fixed tree topology. The improvement is achieved by integrating the DPPDiv code with the Phylogenetic Likelihood Libra ..."
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Abstract—We present a substantially improved and parallelized version of DPPDiv, a software tool for estimating species divergence times and lineagespecific substitution rates on a fixed tree topology. The improvement is achieved by integrating the DPPDiv code with the Phylogenetic Likelihood Library (PLL), a fast, optimized, and parallelized collection of functions for conducting likelihood computations on phylogenetic trees. We show that, integrating the PLL into a likelihoodbased application is straightforward since it took the first author (DD) a programming effort of only one month, without having prior knowledge of DPPDiv, nor the PLL. We achieve sequential speedups that range between a factor of two to three and nearoptimal parallel speedups up to 48 threads on sufficiently large datasets. Hence, with a programming effort of one month, we were able to improve DPPDiv’s timetosolution on parallel systems by two orders of magnitude and also to substantially improve its ability to infer divergence times on largescale datasets. Keywordsphylogenetics; parallel computing; divergence time estimation; programming effort; phylogenetic likelihood I.
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"... Supplementary Information Bayesian estimation of divergence times The objective of the Bayesian analysis is the estimation of the posterior probability, f (t,r,θD), of divergence times t, molecular evolutionary rates r, and model parameters θ, given the molecular data D. This posterior distribution ..."
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Supplementary Information Bayesian estimation of divergence times The objective of the Bayesian analysis is the estimation of the posterior probability, f (t,r,θD), of divergence times t, molecular evolutionary rates r, and model parameters θ, given the molecular data D. This posterior distribution is given by the Bayes theorem[1] f (t,r,θD) ∝ f (θ) f (t) f (rt,θ) f (Dt,r,θ) (1) where f (θ) is the prior of model parameters; f (t) is the prior of times; f (rt,θ) is the prior of rates on the tree; and f (Dt,r,θ) is the likelihood, or the probability of the molecular data given the times, rates, and model parameters. The posterior is generated by MCMC sampling. In this study we faced two important challenges in using eq. (1). The first challenge was constructing the time prior, f (t) = f (tC) fBD(t ¯C tC), (2) which has two components: the density of ages for nodes in the tree for which fossil calibrations are available, f (tC); and the conditional density, based on the birth and death (BD) process, for those nodes where no fossil calibrations are available, fBD(t ¯C tC). The time prior must comply with the requirement that any node cannot be older than its ancestral nodes. During the MCMC iteration, node ages that violate this requirement are never proposed. Effectively f (tC) is
MCMCTree tutorials
"... It is assumed that you have some basic knowledge of using the command line in Windows or Unix systems (e.g. Linux and MacOS). You need to download and install the PAML package from ..."
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It is assumed that you have some basic knowledge of using the command line in Windows or Unix systems (e.g. Linux and MacOS). You need to download and install the PAML package from
www.sciencemag.org/content/346/6215/1320/suppl/DC1 Supplementary Materials for
"... Wholegenome analyses resolve early branches in the tree of life of modern birds ..."
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Wholegenome analyses resolve early branches in the tree of life of modern birds
として，配列アライメン ト ( 塩基かアミノ酸配 列)，化石制約付きの系統樹，および解析
, 2013
"... 解析されており，PAML [8] パッケー ジ (examples/DatingSoftBound) で配信されてい ..."
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Molecular Evolution of Hemagglutinin (H) Gene in Measles Virus Genotypes D3, D5, D9, and H1
"... We studied the molecular evolution of H gene in four prevalent Asian genotypes (D3, D5, D9, and H1) of measles virus (MeV). We estimated the evolutionary time scale of the gene by the Bayesian Markov Chain Monte Carlo (MCMC) method. In addition, we predicted the changes in structure of H protein due ..."
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We studied the molecular evolution of H gene in four prevalent Asian genotypes (D3, D5, D9, and H1) of measles virus (MeV). We estimated the evolutionary time scale of the gene by the Bayesian Markov Chain Monte Carlo (MCMC) method. In addition, we predicted the changes in structure of H protein due to selective pressures. The phylogenetic tree showed that the first division of these genotypes occurred around 1931, and further division of each type in the 1960–1970s resulted in four genotypes. The rate of molecular evolution was relatively slow (5.5761024 substitutions per site per year). Only two positively selected sites (F476L and Q575K) were identified in H protein, although these substitutions might not have imparted significant changes to the structure of the protein or the epitopes for phylactic antibodies. The results suggested
Distributed under Creative Commons CCBY 4.0 OPEN ACCESS
, 2016
"... Declarations can be found on page 13 DOI 10.7717/peerj.1744 Copyright 2016 LossOliveira et al. ..."
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Declarations can be found on page 13 DOI 10.7717/peerj.1744 Copyright 2016 LossOliveira et al.