Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult
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Benoit Morel | Alexey M. Kozlov | Alexandros Stamatakis | Alexey M Kozlov | Pavlos Pavlidis | Lucas Czech | Lukas Hübner | Sarah Lutteropp | Pierre Barbera | Dimitrios Paraskevis | Ben Bettisworth | A. Stamatakis | P. Pavlidis | E. Kostaki | Lucas Czech | D. Paraskevis | Benoit Morel | P. Barbera | S. Lutteropp | Dora Serdari | Evangelia-Georgia Kostaki | Ioannis Mamais | I. Mamais | Ben Bettisworth | Lukas Hübner | Dora Serdari
[1] Yuelong Shu,et al. GISAID: Global initiative on sharing all influenza data – from vision to reality , 2017, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.
[2] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[3] B. Foley,et al. Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 , 2020, Journal of medical virology.
[4] H. Guohu,et al. Spread dynamics of SARS-CoV-2 epidemic in China: a phylogenetic analysis , 2020, medRxiv.
[5] Alexandros Stamatakis,et al. Phylogenetic Search Algorithms for Maximum Likelihood , 2010 .
[6] Maurizio Zazzi,et al. A novel methodology for large-scale phylogeny partition , 2011, Nature communications.
[7] F. Balloux,et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 , 2020, Infection, Genetics and Evolution.
[8] A. Stamatakis,et al. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV , 2019, PeerJ.
[9] Alexandros Stamatakis,et al. A fast and memory-efficient implementation of the transfer bootstrap , 2019, Bioinformatics.
[10] Alexey M. Kozlov,et al. A fast and memory-efficient implementation of the transfer bootstrap , 2019, bioRxiv.
[11] A. Salas,et al. Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders , 2020, Genome research.
[12] A. Stamatakis,et al. Root Digger: a root placement program for phylogenetic trees , 2020, BMC Bioinformatics.
[13] Alexey M. Kozlov,et al. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference , 2018, bioRxiv.
[14] Darren L. Smith,et al. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 , 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.
[15] W. Hanage,et al. Phylogenetic interpretation during outbreaks requires caution , 2020, Nature Microbiology.
[16] Ziding Zhang,et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins , 2020, Nature.
[17] Alexandros Stamatakis,et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models , 2019 .
[18] P. Lemey,et al. Temporal signal and the phylodynamic threshold of SARS-CoV-2 , 2020, bioRxiv.
[19] J. Rougemont,et al. A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.
[20] Benoit Morel,et al. EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences , 2018, bioRxiv.
[21] Gintaras Deikus,et al. Introductions and early spread of SARS-CoV-2 in the New York City area , 2020, Science.
[22] Jianguo Wu,et al. Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 , 2020, Journal of medical virology.
[23] M. Suchard,et al. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. , 2020, bioRxiv.
[24] R. Nielsen,et al. Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny , 2020, bioRxiv.
[25] A. Rodrigo,et al. Likelihood-based tests of topologies in phylogenetics. , 2000, Systematic biology.
[26] Rob DeSalle,et al. How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. , 2007, Systematic biology.
[27] A. Brufsky. Distinct viral clades of SARS‐CoV‐2: Implications for modeling of viral spread , 2020, Journal of medical virology.
[28] Nathan M. Young,et al. Primate molecular divergence dates. , 2006, Molecular phylogenetics and evolution.
[29] D. Montefiori,et al. Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 , 2020, bioRxiv.
[30] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[31] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[32] E. Holmes,et al. The proximal origin of SARS-CoV-2 , 2020, Nature Medicine.
[33] Jason D. Fernandes,et al. Stability of SARS-CoV-2 phylogenies , 2020, bioRxiv.
[34] J. Glenn Morris,et al. Collection of SARS-CoV-2 Virus from the Air of a Clinic within a University Student Health Care Center and Analyses of the Viral Genomic Sequence , 2020 .
[35] Hidetoshi Shimodaira,et al. Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.
[36] D. Robinson,et al. Comparison of phylogenetic trees , 1981 .
[37] Kari Stefansson,et al. Spread of SARS-CoV-2 in the Icelandic Population , 2020, The New England journal of medicine.
[38] G. Whittaker,et al. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop , 2020, Journal of Molecular Biology.
[39] Alexandros Stamatakis,et al. Methods for automatic reference trees and multilevel phylogenetic placement , 2018, bioRxiv.
[40] Edward C. Holmes,et al. A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology , 2020, bioRxiv.
[41] Nuno R. Faria,et al. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage , 2020, medRxiv.
[42] Alexey M. Kozlov,et al. ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes , 2018, bioRxiv.
[43] David L Robertson,et al. No evidence for distinct types in the evolution of SARS-CoV-2 , 2020, Virus evolution.
[44] Alexandros Stamatakis,et al. Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data , 2020, Bioinform..
[45] A. von Haeseler,et al. UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.
[46] Trevor Bedford,et al. Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.
[47] Kai Zhao,et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.
[48] Jiajie Zhang,et al. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo , 2016, bioRxiv.
[49] M. Salemi,et al. A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis , 2020, JMIR public health and surveillance.
[50] E. Holmes,et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding , 2020, The Lancet.
[51] A. Rambaut,et al. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence , 2020, medRxiv.
[52] Samantha Lycett,et al. Automated analysis of phylogenetic clusters , 2013, BMC Bioinformatics.