Assume we are given an optimal MSA
and assume further
that we know the tree
Each indel event can be mapped
to exactly one edge in the tree (see Figure ).
The result of a deletion event are gaps that appear in all
of the subtree where the event took
place. In contrast, when the event was an insertion, gaps appear
in all sequences that are not in the subtree below the event.
In the alignment of Figure , there are 4 indel
events, which we call gap blocks (see Definition
). The first gap block consists of two gaps that
appear in sequences A and B. If x is the ancestor of all the
sequences, then the event must either be a deletion in the
ancestor of sequences A and B, or it can be an insertion on the
Accordingly, event 2 is an insertion in
sequence D, event 3 represents a deletion in the ancestor of D and
E, and finally event 4 is an insertion in sequence C.
Indel events are shown in
the evolutionary tree (right) of the MSA (left).