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Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees.
Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees.
- Source :
- Molecular Biology & Evolution; Dec2021, Vol. 38 Issue 12, p5819-5824, 6p
- Publication Year :
- 2021
-
Abstract
- The vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees inferred with unrestricted public sequences, which we update daily to incorporate new sequences. Our database uses the recently proposed mutation-annotated tree (MAT) format to efficiently encode the tree with branches labeled with parsimony-inferred mutations, as well as Nextstrain clade and Pango lineage labels at clade roots. As of June 9, 2021, our SARS-CoV-2 MAT consists of 834,521 sequences and provides a comprehensive view of the virus' evolutionary history using public data. We also present matUtils—a command-line utility for rapidly querying, interpreting, and manipulating the MATs. Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER%5fSARS-CoV-2/ and https://github.com/yatisht/usher , respectively. [ABSTRACT FROM AUTHOR]
- Subjects :
- DATABASES
SARS-CoV-2
SURVEILLANCE detection
PARSIMONIOUS models
COVID-19
Subjects
Details
- Language :
- English
- ISSN :
- 07374038
- Volume :
- 38
- Issue :
- 12
- Database :
- Complementary Index
- Journal :
- Molecular Biology & Evolution
- Publication Type :
- Academic Journal
- Accession number :
- 154512835
- Full Text :
- https://doi.org/10.1093/molbev/msab264