The abundance based indices measure either diversity number and

Population nucleotide CHMFL-ABL-053 or index π measures the average number of nucleotide differences between any two genomes of the quasispecies (Nei, 1987 and Nei and Kumar, 2000) (Equation IVb). Pair-wise differences have been traditionally evaluated by the Hamming distance (number of mutations that distinguish a pair of sequences), although any substitution model (JC69, K80, F81, etc.) [(Nei and Kumar, 2000) among others] or subsets of differences (transitions or transversions, synonymous or non-synonymous mutations) may be considered. Index π provides more valuable information than Mf because it takes into account the differences between any two genomes in the population.
The Simpson index, HSi (Equation V) is the probability that two randomly selected genomes from a viral population belong to the same haplotype ( Nowak et al., 1991 and Wolinsky et al., 1996). The index was established in ecology to give the probability that two randomly selected individuals from a habitat belong to the same class (Magurran, 2004). In its application to virology, any sampled genome has either the same or a different sequence than a given haplotype. Therefore, if the Simpson index is λ, 1−λ represents the probability that two genomes taken at random belong to a different haplotype. This transformation is known as the Gini-Simpson index, HGS (Equation VIa). The indices just summarized can be applied to sequences sampled either by the cloning-Sanger procedure or new NGS platforms, using specific genomic regions or entire genome sequences.