2. Classical complexity indices used in virology
Fig. 1. Schematic representation of the sequences (reads) obtained from a NGS experiment. Viral genomes are represented as horizontal lines and mutations as different colored symbols on the lines. The sequences are clustered by haplotypes (Hpl). The information obtained from the sequence alignment can be divided into a haplotype alignment (each different sequence CHMFL-ABL-053 counted once), and a vector of frequencies (shows the frequency of different haplotypes).Figure optionsDownload full-size imageDownload high-quality image (575 K)Download as PowerPoint slide
The indices commonly used to compare viral quasispecies diversity are the minimum mutation frequency (Mf min), the maximum mutation frequency (Mf max), the normalized Shannon entropy (HSN), and the nucleotide diversity (π). They have and are still providing extensive information on mutant spectrum complexity both in natural and laboratory samples of viruses [see Domingo et al., (2012) for a review].
Fig. 1. Schematic representation of the sequences (reads) obtained from a NGS experiment. Viral genomes are represented as horizontal lines and mutations as different colored symbols on the lines. The sequences are clustered by haplotypes (Hpl). The information obtained from the sequence alignment can be divided into a haplotype alignment (each different sequence CHMFL-ABL-053 counted once), and a vector of frequencies (shows the frequency of different haplotypes).Figure optionsDownload full-size imageDownload high-quality image (575 K)Download as PowerPoint slide
The indices commonly used to compare viral quasispecies diversity are the minimum mutation frequency (Mf min), the maximum mutation frequency (Mf max), the normalized Shannon entropy (HSN), and the nucleotide diversity (π). They have and are still providing extensive information on mutant spectrum complexity both in natural and laboratory samples of viruses [see Domingo et al., (2012) for a review].