Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters

Journal Article · 09 February 2025 · Bioinformatics Advances

DOI: https://doi.org/10.1093/bioadv/vbaf025 · OSTI ID:2520209

Lapp, Zena Malakie  ^[1]; Yoon, Hyejin  ^[1]; Foley, Brian Thomas  ^[1]; Leitner, Thomas Kenneth  ^[1]

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1. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Motivation: The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference. Two versions of this method are available as a webtool. Neither of these methods consider multistate characters or gaps in the sequence alignment. Results: Here, we present an updated, user-friendly web and command-line version of Hypermut with functionality to handle multistate characters and gaps in the sequence alignment. This tool allows for straightforward integration of hypermutation detection into sequence analysis pipelines. As with the previous tool, while the main purpose is to identify G to A hypermutation events, any mutational pattern and context can be specified. Availability and implementation: Hypermut 3 is written in Python 3. It is available as a command-line tool at https://github.com/MolEvolEpid/hypermut3 and as a webtool at https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermutv3.html.

• Research Organization: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: National Institutes of Health (NIH); USDOE; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE National Nuclear Security Administration (NNSA)
• Grant/Contract Number: 89233218CNA000001
• OSTI ID: 2520209
• Report Number(s): LA-UR--24-31336
• Journal Information: Bioinformatics Advances, Journal Name: Bioinformatics Advances Journal Issue: 1 Vol. 5; ISSN 2635-0041
• Publisher: Oxford University PressCopyright Statement
• Country of Publication: United States
• Language: English