Purpose: This interface takes a nucleotide alignment and documents the nature and context of nucleotide substitutions in a sequence population relative to a reference sequence.
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: Please reference these articles when using Hypermut:
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 |