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GPL-3.0-only licensed by Christian Hoener zu Siederdissen, 2013-2017
A selection of (sequence) alignment algorithms. Both terminal,
and syntactic variables, as well as the index type is not fixed
here. This makes it possible to select the correct structure of
the grammar here, but bind the required data type for alignment
in user code.
That being said, these algorithms are mostly aimed towards
sequence alignment problems.
List of grammars for sequences:
global alignment
linear scoring: Needleman-Wunsch style
affine scoring: Gotoh
semiglobal alignment
overhang alignment
List of grammar for trees:
global alignment
linear scoring
affine scoring
simplified affine scoring
global editing
linear scoring
We now provide tree alignment and editing algorithms as well.
We do not depend on ADPfusionForest to achieve this because
grammar rules are completely disconnected from the underlying
ADPfusion machinery.