The AlignmentAlgorithms package
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
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.
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|Versions||0.0.1.0, 0.0.1.2, 0.0.2.0, 0.0.2.1, 0.1.0.0|
|Dependencies||ADPfusion (==0.5.2.*), base (>=4.7 && <5.0), containers (>=0.5), fmlist (>=0.9), FormalGrammars (==0.3.1.*), GrammarProducts (==0.1.1.*), PrimitiveArray (==0.8.0.*), vector (>=0.10) [details]|
|Copyright||Christian Hoener zu Siederdissen, 2013-2017|
|Author||Christian Hoener zu Siederdissen, 2013-2017|
|Category||Algorithms, Data Structures, Bioinformatics, Linguistics|
|Source repository||head: git clone git://github.com/choener/AlignmentAlgorithms|
|Uploaded||Tue Mar 14 14:41:48 UTC 2017 by ChristianHoener|
|Downloads||539 total (47 in the last 30 days)|
|Status||Docs available [build log]
Last success reported on 2017-03-14 [all 1 reports]
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