How can I determine the subtype/clade of my HIV sequences?
There are many tools that can help you identify the subtype/clade. Each tool has its pros and cons. Some can handle many sequences at once, while some can only analyze one sequence at a time. • Recombinant Identification Program (RIP) (HIV Databases) • TreeMaker (HIV Databases) • HIV BLAST (HIV Databases) • BLAST-based HIV-1 Subtyping Tool (NCBI) • Phylogenetic-based REGA Subtyping Tools (Bio-Africa) The Recombinant Identification Program (RIP) is a program developed at the HIV Database to identify sequences that appear to be mosaics of distinct phylogenetic clades. The idea is that such mosaic sequences are likely recombinants. RIP was designed to detect recombinants of sequences belonging to different subtypes of HIV-1, in response to the identification of intersubtype recombination as an important source of new variation in HIV-1, but it can be used for other applications, including analysis of non-HIV sequences. For additional details, see RIP Explanation.
Related Questions
- Why is the subtype B consensus sequence used rather than a particular isolate, the consensus sequence for a different subtype, or the consensus sequence for Group M sequences?
- How do I obtain an alignment of all sequences of a particular gene with a particular subtype or country of origin?
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