Purpose: To document the nature and context of nucleotide substitutions in a sequence population relative to a reference sequence. See details below. For a simple "quick and dirty" scan for hypermutants, try the QC Tool.
These options apply only to Hypermut 2.0 analysis, and have no effect on the Original Hypermut output. For typical analyses of APOBEC-induced hypermutation in HIV, these options should be left in their default settings. | |||||
Mutation | |||||
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Upstream context: | ↓ |
Downstream context: | Enforce context: | ||
Customize Hypermut pattern: | ↓ |
On reference sequence On both sequences On query sequence | |||
Customize control pattern: | ↓ |
Analyses to perform: | Both Original Hypermut Hypermut 2.0 |
Details: The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. Please choose the reference sequence carefully. For example, for an intrapatient set, the reference should probably be the most common form in the first sampled time point; for a set of unrelated sequences, the reference should probably be the consensus sequence for the appropriate subtype. Before using, please read:
References: