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bioRxiv · 10.1101/2021.04.03.438321

matUtils: Tools to Interpret and Manipulate Mutation Annotated Trees

McBroome, J.·Thornlow, B.·Hinrichs, A. S.·De Maio, N.·Goldman, N.·Haussler, D.·Corbett-Detig, R.·Turakhia, Y.
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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_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.

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McBroome, J., Thornlow, B., Hinrichs, A. S., De Maio, N., Goldman, N., Haussler, D., Corbett-Detig, R., Turakhia, Y.. 2021-04-04. matUtils: Tools to Interpret and Manipulate Mutation Annotated Trees. https://doi.org/10.1101/2021.04.03.438321

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