Some HIV researchers are convinced that careful lab work is enough to prevent contamination. After seeing many examples of contamination pass by, we disagree.
Contamination happens frequently, even in the best laboratories.
Screening for contamination should be done before the analysis of the sequences, and periodically during the course of large sequencing studies, so problems can be detected and corrected early. Following the steps below will help to check your sequences. They are no substitute for common sense and precautions, but they may help reveal contamination in your sequences. Create a phylogenetic tree that includes all the sequences in the study. A phylogenetic tree can clarify the relations between the sequences.