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Gaps and Trees

In contrast to mutations indels do not happen very frequently, and a second indel event at the same place of the same size are very rare. Indels usually have a great impact on the resulting protein structure, whereas a mutation usually has little effect. In the Markovian model of evolution, we assume that mutations can happen anywhere in a protein and are independent of each other. This is a useful and logical assumption, but it is definitely not true for indels [23]. Hence gaps should be treated separately.


Chantal Korostensky