I am working on some specific point mutations in HIV-1 gene. I want to know the prevalence of such mutations in the published sequences.
Check it on the HIV sequence database. You can search by position relative to HXB2, download all the sequences that they have in the database that match that exact position, or (more logically perhaps) the nearby region to have a look that the alignment is reasonable. When you have the alignment, you can check each character. There are also tools for converting to amino acid (HIV align with codon alignment) if you need to look at amino acid mutations.
The QUICKALIGN tool is made to do this:
http://www.hiv.lanl.gov/content/sequence/QUICK_ALIGN/QuickAlign.html
You can search with DNA or protein coordinates, or with a peptide or DNA sequence. On the results page, you can click the "summarize all" or "summarize by subtype"get a summary of the percentage of each base or amino acid at each position.
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