**4.1. Methods for quasispecies reconstruction**

Quasispecies reconstruction refers to the estimation of number of viral variants and their frequency. Each viral variant in a quasispecies is considered as a haplotype. Tools available for this purpose include Short Read Assembly into Haplotypes (ShoRAH) [73], Quasispecies Reconstruction algorithm (QuRe) [74] and QuasiRecomb [75].
