Example 1 (partial set) Tree

This partial dataset contains several examples of possible contamination.

1. Sequences from patient F spread over three clusters. One cluster is very similar to HXB2/LAI and is probably a laboratory contaminant. The distinctness of the other two clusters suggests either dual infection, contamination with an isolate for which there is no sequence in GenBank, or mix-up with a patient that's not in the study.
2. Patients E and G both have a single sequence that clusters tightly with the other patient, suggesting sample mix-up or mislabeling.