About: Fast Whole-Genome Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression

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About: Fast Whole-Genome Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Fast Whole-Genome Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression
Creator	Vitányi, Paul
Source	BioRxiv
abstract	We analyze the whole genome phylogeny and taxonomy of the SARS-CoV-2 virus using compression. This is a new fast alignment-free method called the “normalized compression distance” (NCD) method. It discovers all effective similarities based on Kolmogorov complexity. The latter being incomputable we approximate it by a good compressor such as the modern zpaq. The results comprise that the SARS-CoV-2 virus is closest to the RaTG13 virus and similar to two bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC4. The similarity is quantified and compared with the same quantified similarities among the mtDNA of certain species. We treat the question whether Pangolins are involved in the SARS-CoV-2 virus. The compression method is simpler and possibly faster than any other whole genome method, which makes it the ideal tool to explore phylogeny.
has issue date	2020-08-26(xsd:dateTime)
bibo:doi	10.1101/2020.07.22.216242
has license	biorxiv
sha1sum (hex)	b70851a32fc6ac8148d432ed02884c9c769e804e
schema:url	https://doi.org/10.1101/2020.07.22.216242
resource representing a document's title	Fast Whole-Genome Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression
schema:publication	bioRxiv
resource representing a document's body	covid:b70851a32fc6ac8148d432ed02884c9c769e804e#body_text
is schema:about of	named entity 'SARS-CoV-2' named entity 'Compression' named entity 'CLOSEST' named entity 'COMPRISE' named entity 'APPROXIMATE' named entity 'FAST' named entity 'COMPRESSION' named entity 'SIMILARITY' named entity 'BASED' named entity 'PANGOLINS' named entity 'GOOD' named entity 'faster' named entity 'compression' named entity 'SARS-CoV-2' named entity 'coronaviruses' named entity 'taxonomy' named entity 'compression' named entity 'Phylogeny' named entity 'SARS-CoV-2' named entity 'Kolmogorov complexity' named entity 'bat' named entity 'NCD' named entity 'bat' named entity 'genome' named entity 'Pangolins' named entity 'SARS-CoV-2 virus' named entity 'SARS-CoV-2' named entity 'distance matrix' named entity 'FASTA file format' named entity 'phylogeny' named entity 'fasta' named entity 'Lempel-Ziv' named entity 'bat' named entity 'n 2' named entity 'human mtDNA' named entity 'SARS-CoV-2 virus' named entity 'Gzip' named entity 'Hamming distance' named entity 'distance matrix' named entity 'NCD' named entity 'NCD' named entity 'REMARK' named entity 'phylogeny' named entity 'GISAID' named entity 'SARS-CoV-2 virus' named entity 'Normalized Compression Distance' named entity 'mtDNA' named entity 'COVID-19 pandemic' named entity 'Kolmogorov complexity' named entity 'PPMZ' named entity 'virus' named entity 'genome' named entity 'nucleotides' named entity 'Severe Acute Respiratory Syndrome' named entity 'genome' named entity 'dendrogram' named entity 'Yunnan' named entity 'virus' named entity 'SARS-CoV-2' named entity 'upper semicomputable' named entity 'virus' named entity 'Betacoronavirus' named entity 'Bat' named entity 'sequence database' named entity 'mammal species' named entity 'mtDNA' named entity 'Kolmogorov complexity' named entity 'NCD' named entity 'phylogeny' named entity 'data compression' named entity 'sequenced' named entity 'SARS-CoV-2' named entity 'GenBank' named entity 'SARS-CoV-2' named entity 'GISAID' named entity 'SARS-CoV-2 virus' named entity 'SARS-CoV-2 virus' named entity 'mitochondrial genomes' named entity 'Kolmogorov complexity' named entity 'SARS virus' named entity 'RNA' named entity 'upper semicomputable' named entity 'NCD' named entity 'NCD'

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