The comparison of BCV main sequence assembling results with sequences of cloned PCR products.

<p>Phylogenetic tree shows relationships between consensus sequences (black squares) assembled from direct reads of the HIV protease gene fragment with sequences of clones (black circles) for sample GEN014DR.01A. The consensus assembled from two opposite direct reads with trimmed degenerate parts is denoted as D.vqa01; the one that is assembled by the BCV indel detection script is FR.main. F.main is the dominating DNA type extracted from a direct read in the forward direction by the BCV indel detection script; R.main is the same read in the opposite direction. H61 is the blastn best hit to sequence D.vqa01 used for scaling quasispecies variation (black circles).Reads in forward and reverse directions have different fractions of non-degenerate positions: F: 56/503 = 11%; R –430/492 = 87%. B: a node in the tree corresponding to HIV subtype B branch. The phylogenetic tree is constructed by the Minimum Evolution method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054835#pone.0054835-Rzhetsky1" target="_blank">[66]</a> for the Maximum Composite Likelihood <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054835#pone.0054835-Tamura1" target="_blank">[67]</a> distance matrix by the MEGA 5 software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054835#pone.0054835-Tamura2" target="_blank">[68]</a>.