The principle of the Three-Way-Alignment is to build up a multiple alignment by
constructing a tree and aligning sequences and pre-aligned
groups of sequences simultaneously:
Given N sequences and assume, that there is a tree topology for sequences and a multiple alignment for n sequences coupled to the tree, i.e n=5:
Each edge of the tree is tested for an insertion of a new sequence, i.e. test edge e:
For an insertion of a sequence in edge e, a three-way-alignment between
the following groups of sequences is computed
- The aligned sequences on the left of e
- The aligned sequences on the right of e
- the new sequence
The three-way alignment implies new edge weights and therefore a new path length
for the complete tree:
In order to keep the amount of evolution as small as possible,
one chooses the topology resulting in the smallest path length.
In the example an alignment of n+1 sequences now is coupled with a tree
topology for six sequences:
and a new sequence may be inserted...
When constructing a multiple alignment iteratively in this way,
a correction of positions in the profile alignments is possible.
For a more detailed view on the subject, have a look at the paper
of Vingron and v. Haeseler.