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Updated: Nov 10, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees.

Jakob McBroome^1,2, Bryan Thornlow^1,2, Angie S Hinrichs²

¹Department of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA.

Biorxiv : the Preprint Server for Biology

|April 6, 2021

Summary

This summary is machine-generated.

A new database of SARS-CoV-2 phylogenetic trees, using the mutation-annotated tree (MAT) format, offers a comprehensive view of viral evolution. This daily updated resource, alongside the matUtils tool, aids in analyzing vast sequencing data.

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Area of Science:

Virology
Computational Biology
Genomics

Background:

The exponential growth of SARS-CoV-2 sequencing data presents significant challenges for comprehensive analysis with existing bioinformatics tools.
Efficiently tracking the evolutionary trajectory of SARS-CoV-2 requires novel data structures and analytical approaches.

Approach:

Development of a daily updated database of SARS-CoV-2 phylogenetic trees utilizing the mutation-annotated tree (MAT) format.
Incorporation of parsimony-inferred mutations, Nextstrain clades, and Pango lineages within the MAT format for detailed evolutionary annotation.
Creation of `matUtils`, a command-line utility for efficient querying, interpretation, and manipulation of MAT data.

Key Points:

The SARS-CoV-2 MAT database, as of June 9, 2021, contained 834,521 sequences, providing an extensive representation of the virus's evolutionary history.
The MAT format enables efficient encoding of phylogenetic trees with rich mutational and lineage information.
`matUtils` facilitates rapid analysis and manipulation of large-scale phylogenetic datasets.

Conclusions:

The developed SARS-CoV-2 MAT database and `matUtils` provide a scalable solution for analyzing the rapidly expanding volume of viral sequencing data.
These resources offer a valuable tool for researchers studying SARS-CoV-2 evolution, epidemiology, and the emergence of new variants.
The daily updates ensure that the database reflects the most current understanding of SARS-CoV-2's phylogenetic landscape.