They are no substitute for common sense and precautions, but they may help spot contamination in your sequences. Create a phylogenetic tree that includes all the sequences in the study. A phylogenetic tree clarifies the relations between the sequences. If you have lab strain contamination or sample mix-ups between two patients, a phylogenetic tree will likely show it. Once you have your sequences aligned, generate a simple neighbor joining tree to check for potential problems.
Blast is a program that finds sequences with very high similarity to the query sequence.
If your sequence is very similar to a published strain, especially a lab strain that is used for in vitro studies, it is likely that you have contamination. Even if your sequence is not identical to the lab strain, watch out for in vitro recombination, where only part of the sequence matches the lab strain, and the other part is derived from your patient sample. We've prepared some basic guidelines . Look carefully at the alignments, and pay attention to patient signature patterns. Signature patterns often help to show what is 'typical' and 'atypical' for a patient, and thus help to recognize sequences that don't seem to belong with a patient.