Hypermut 3

Hypermut 3 detects specific mutational patterns in nucleotide sequences, particularly for identifying hypermutation events induced by APOBEC3F and APOBEC3G.

Key Features:

• Multistate character handling: Processes multistate characters in sequence alignments.
• Gap handling: Handles gaps in sequence alignments.
• Customizable mutational patterns: Allows specification of any mutational pattern and nucleotide context, with default detection of G to A hypermutation events.
• Dual implementation: Available as both a command-line tool and a web application.

Scientific Applications:

• Hypermutated sequence identification: Identifies sequences containing APOBEC3F- and APOBEC3G-induced mutations that are not representative of viral evolution.
• Sequence analysis pipeline integration: Enables straightforward incorporation of hypermutation detection into downstream sequence analysis workflows.
• Viral sequence quality control: Flags hypermutated sequences to prevent distortion of evolutionary analyses.

Methodology:

Hypermut 3 detects hypermutation events in sequences relative to a reference sequence.