<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Morel, B.</style></author><author><style face="normal" font="default" size="100%">Barbera, P.</style></author><author><style face="normal" font="default" size="100%">Czech, L.</style></author><author><style face="normal" font="default" size="100%">Bettisworth, B.</style></author><author><style face="normal" font="default" size="100%">Hübner, L.</style></author><author><style face="normal" font="default" size="100%">Lutteropp, S.</style></author><author><style face="normal" font="default" size="100%">Serdari, D.</style></author><author><style face="normal" font="default" size="100%">Kostaki, E. G.</style></author><author><style face="normal" font="default" size="100%">Mamais, I.</style></author><author><style face="normal" font="default" size="100%">Kozlov, A. M.</style></author><author><style face="normal" font="default" size="100%">Pavlidis, P.</style></author><author><style face="normal" font="default" size="100%">Paraskevis, D</style></author><author><style face="normal" font="default" size="100%">Stamatakis, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic analysis of SARS-CoV-2 data is difficult</style></title><secondary-title><style face="normal" font="default" size="100%">Mol Biol EvolMol Biol EvolMol Biol Evol</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Molecular biology and evolution</style></alt-title><short-title><style face="normal" font="default" size="100%">Molecular biology and evolutionMolecular biology and evolution</style></short-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">outgroups</style></keyword><keyword><style  face="normal" font="default" size="100%">phylogenetic inference</style></keyword><keyword><style  face="normal" font="default" size="100%">phylogeny rooting</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2</style></keyword><keyword><style  face="normal" font="default" size="100%">strain classification</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Dec 15</style></date></pub-dates></dates><edition><style face="normal" font="default" size="100%">2020/12/15</style></edition><isbn><style face="normal" font="default" size="100%">0737-4038</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.</style></abstract><accession-num><style face="normal" font="default" size="100%">33316067</style></accession-num><notes><style face="normal" font="default" size="100%">1537-1719Morel, BenoitBarbera, PierreCzech, LucasBettisworth, BenHübner, LukasLutteropp, SarahSerdari, DoraKostaki, Evangelia-GeorgiaMamais, IoannisKozlov, Alexey MPavlidis, PavlosParaskevis, DimitriosStamatakis, AlexandrosJournal ArticleUnited StatesMol Biol Evol. 2020 Dec 15:msaa314. doi: 10.1093/molbev/msaa314.</style></notes><auth-address><style face="normal" font="default" size="100%">Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.Department of Health Sciences, European University Cyprus, Nicosia-Cyprus.Institute of Computer Science, Foundation for Research and Technology-Hellas, Crete, Greece.</style></auth-address><remote-database-provider><style face="normal" font="default" size="100%">NLM</style></remote-database-provider></record></records></xml>