Intro | Install package | Data | Collapsing reads to haplotypes | Forward and reverse strand haplotype intersection | Simulate quasispecies data | Quasispecies data exploration | Quasispecies complexity by biodiversity indices | Genotyping

Quasispecies complexity by biodiversity indices | Incidence-based diversity indices or richness indices | Abundance-based diversity indices | Functional diversity | Incidence-based functional diversity indices | Abundance-based functional diversity indices | Sample size and bias | The load of rare haplotypes

Introduction | Install package | Abundance | Powers of a fraction | Geometric sequence | Random genomes and variant haplotypes | Generate a quasispecies of acute infection | Generate a quasispecies of chronic infection | Diverging populations | References