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5.5. Differences are not always what they look like
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The algorithm we have presented works on an array of distance between sequences. These distances are evaluated on the basis of differences between the sequences. The problem is that behind the differences we observed on the set of sequences, there may beother mutations which cannot be observed and we should modify the distances. We will have a look at some simple cases of these observed differences which may correspond to hidden differences and then we will see how the evaluation, computationof the number of differences may be affected. The simple case is this one, aunique substitution between, in the sequence One we have a Cand it turns out that in the sequence Two, there is a mutation, C becomes A. So what we observed is one mutation and the actual substitution is also one. Let's look, here we have two sequencesand here we have a mutation. OK. One difference, one mutation so in that case it's correct. A first case in which there is a discrepancy between the substitutions, number of substitutions beingobserved and the number of actual substitutions is in the case of multiple substitutions. In the first sequence there isan A, it's OK, in the second sequence the A mutates in C andthen in T so what we will see is only one difference, one substitution when there is actually two.
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