标题
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
作者
关键词
Phylogenetic analysis, Phylogenetics, Genetic loci, Simulation and modeling, Gene flow, Genetic networks, Network analysis, Evolutionary genetics
出版物
PLoS Computational Biology
Volume 15, Issue 4, Pages e1006650
出版商
Public Library of Science (PLoS)
发表日期
2019-04-09
DOI
10.1371/journal.pcbi.1006650
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Bayesian reconstruction of transmission within outbreaks using genomic variants
- (2018) Nicola De Maio et al. PLoS Computational Biology
- Local and relaxed clocks: the best of both worlds
- (2018) Mathieu Fourment et al. PeerJ
- P3: Phylogenetic Posterior Prediction in RevBayes
- (2017) Sebastian Höhna et al. MOLECULAR BIOLOGY AND EVOLUTION
- The Structured Coalescent and Its Approximations
- (2017) Nicola F. Müller et al. MOLECULAR BIOLOGY AND EVOLUTION
- StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates
- (2017) Huw A. Ogilvie et al. MOLECULAR BIOLOGY AND EVOLUTION
- Why Concatenation Fails Near the Anomaly Zone
- (2017) Fábio K. Mendes et al. SYSTEMATIC BIOLOGY
- Taming the BEAST—A Community Teaching Material Resource for BEAST 2
- (2017) Joëlle Barido-Sottani et al. SYSTEMATIC BIOLOGY
- Inferring Ancestral Recombination Graphs from Bacterial Genomic Data
- (2016) Timothy G. Vaughan et al. GENETICS
- Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent
- (2016) Graham Jones JOURNAL OF MATHEMATICAL BIOLOGY
- Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
- (2016) Denise Kühnert et al. MOLECULAR BIOLOGY AND EVOLUTION
- Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika
- (2016) Hugo F. Gante et al. MOLECULAR ECOLOGY
- Evolution of the immune system influences speciation rates in teleost fishes
- (2016) Martin Malmstrøm et al. NATURE GENETICS
- After Ebola in West Africa — Unpredictable Risks, Preventable Epidemics
- (2016) NEW ENGLAND JOURNAL OF MEDICINE
- Fungal-algal association patterns in lichen symbiosis linked to macroclimate
- (2016) Garima Singh et al. NEW PHYTOLOGIST
- Gene Tree Discordance Causes Apparent Substitution Rate Variation
- (2016) Fábio K. Mendes et al. SYSTEMATIC BIOLOGY
- Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods
- (2016) Huw A. Ogilvie et al. SYSTEMATIC BIOLOGY
- RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
- (2016) Sebastian Höhna et al. SYSTEMATIC BIOLOGY
- SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
- (2016) Nicola De Maio et al. PLoS Computational Biology
- Inferring Ancestral Recombination Graphs from Bacterial Genomic Data
- (2016) Timothy G. Vaughan et al. GENETICS
- Phylogeography by diffusion on a sphere: whole world phylogeography
- (2016) Remco Bouckaert PeerJ
- West African Ebola Epidemic after One Year — Slowing but Not Yet under Control
- (2015) NEW ENGLAND JOURNAL OF MEDICINE
- Synthesis of phylogeny and taxonomy into a comprehensive tree of life
- (2015) Cody E. Hinchliff et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Total-Evidence Dating under the Fossilized Birth–Death Process
- (2015) Chi Zhang et al. SYSTEMATIC BIOLOGY
- PoMo: An Allele Frequency-Based Approach for Species Tree Estimation
- (2015) Nicola De Maio et al. SYSTEMATIC BIOLOGY
- Which Phylogenetic Networks are Merely Trees with Additional Arcs?
- (2015) Andrew R. Francis et al. SYSTEMATIC BIOLOGY
- Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
- (2015) Sebastien Roch et al. THEORETICAL POPULATION BIOLOGY
- New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation
- (2015) Nicola De Maio et al. PLoS Genetics
- DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent
- (2014) Graham Jones et al. BIOINFORMATICS
- Efficient Bayesian inference under the structured coalescent
- (2014) Timothy G. Vaughan et al. BIOINFORMATICS
- Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model
- (2014) D. Kuhnert et al. Journal of the Royal Society Interface
- Infectious disease: Tough choices to reduce Ebola transmission
- (2014) Christopher J. M. Whitty et al. NATURE
- The genomic substrate for adaptive radiation in African cichlid fish
- (2014) David Brawand et al. NATURE
- The fossilized birth-death process for coherent calibration of divergence-time estimates
- (2014) T. A. Heath et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
- (2014) Remco Bouckaert et al. PLoS Computational Biology
- Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
- (2014) Alexandra Gavryushkina et al. PLoS Computational Biology
- Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2
- (2014) Philippe Lemey et al. PLoS Pathogens
- Evolutionary rates and HBV: issues of rate estimation with Bayesian molecular methods
- (2013) Remco Bouckaert et al. ANTIVIRAL THERAPY
- Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models
- (2013) Nicola De Maio et al. MOLECULAR BIOLOGY AND EVOLUTION
- A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics
- (2013) T. G. Vaughan et al. MOLECULAR BIOLOGY AND EVOLUTION
- Posterior Predictive Bayesian Phylogenetic Model Selection
- (2013) Paul O. Lewis et al. SYSTEMATIC BIOLOGY
- The Influence of Gene Flow on Species Tree Estimation: A Simulation Study
- (2013) Adam D. Leaché et al. SYSTEMATIC BIOLOGY
- Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
- (2012) David Bryant et al. MOLECULAR BIOLOGY AND EVOLUTION
- Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
- (2012) T. Stadler et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mapping the Origins and Expansion of the Indo-European Language Family
- (2012) R. Bouckaert et al. SCIENCE
- A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
- (2012) Fredrik Ronquist et al. SYSTEMATIC BIOLOGY
- Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo
- (2011) Chieh-Hsi Wu et al. GENETICS
- Complex Population Dynamics and the Coalescent Under Neutrality
- (2011) Erik M. Volz GENETICS
- Estimating the Basic Reproductive Number from Viral Sequence Data
- (2011) Tanja Stadler et al. MOLECULAR BIOLOGY AND EVOLUTION
- Inference of human population history from individual whole-genome sequences
- (2011) Heng Li et al. NATURE
- Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation
- (2011) Joseph Heled et al. SYSTEMATIC BIOLOGY
- Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia
- (2011) R. Alexander Pyron SYSTEMATIC BIOLOGY
- Bayesian random local clocks, or one rate to rule them all
- (2010) Alexei J Drummond et al. BMC BIOLOGY
- Sampling-through-time in birth–death trees
- (2010) Tanja Stadler JOURNAL OF THEORETICAL BIOLOGY
- Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time
- (2010) P. Lemey et al. MOLECULAR BIOLOGY AND EVOLUTION
- Choosing among Partition Models in Bayesian Phylogenetics
- (2010) Y. Fan et al. MOLECULAR BIOLOGY AND EVOLUTION
- Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
- (2010) Wangang Xie et al. SYSTEMATIC BIOLOGY
- On incomplete sampling under birth–death models and connections to the sampling-based coalescent
- (2009) Tanja Stadler JOURNAL OF THEORETICAL BIOLOGY
- Bayesian Inference of Species Trees from Multilocus Data
- (2009) J. Heled et al. MOLECULAR BIOLOGY AND EVOLUTION
- Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework
- (2009) Erik W. Bloomquist et al. SYSTEMATIC BIOLOGY
- Gene tree discordance, phylogenetic inference and the multispecies coalescent
- (2009) James H. Degnan et al. TRENDS IN ECOLOGY & EVOLUTION
- Bayesian Phylogeography Finds Its Roots
- (2009) Philippe Lemey et al. PLoS Computational Biology
- Bayesian inference of fine-scale recombination rates using population genomic data
- (2008) Y. Wang et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
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