Dinucleotide composition has been recognized as a species-specific characteristic of organisms for more than 20 years. Lang (2000, Bioinformatics, 16, 212-221), found that in Monilinia rRNA a species-specific identity is conserved when dinucleotide counts are compressed into net dinucleotide counts (e.g., 50AC + 20CA = 30nAC) and clusters of net dinucleotides of equal value (e.g., 30nAC + 30nCT + 30nTA = 30ACTA) which were called circuits. This study evaluates circuit assemblages (CAs)--the collection of all net dinucleotide circuits derived from a sequence--in a diverse set of 110 HIV-1 genomes. The circuit composition, which is often based on
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