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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
1999-07-14