Additional file 3.

Phylogenetic trees reconstructed from sequences obtained from patient P47 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P47 (ETR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. Sequence with nonsense mutation is colored in blue. The clades selected for selective pressure analysis are indicated by a gray line (clade 1, ω = 0.2487 and clade 2, ω = 0.7177).

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Jardim et al. BMC Infectious Diseases 2013 13:61   doi:10.1186/1471-2334-13-61