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HIVCD is an informatics tool developed to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. Full details can be found in our paper titled "Application of a new informatics tool for contamination screening in the HIV sequencing laboratory"
The code provided is a simple user interface to the underlying algorithm. We provide it as a convenience but it comes with absolutely no warranty as stated in the Apache License, Version 2.0.
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