name: AlignmentAlgorithms
version: 0.1.0.0
author: Christian Hoener zu Siederdissen, 2013-2017
copyright: Christian Hoener zu Siederdissen, 2013-2017
homepage: https://github.com/choener/AlignmentAlgorithms
bug-reports: https://github.com/choener/AlignmentAlgorithms/issues
maintainer: choener@bioinf.uni-leipzig.de
category: Algorithms, Data Structures, Bioinformatics, Linguistics
license: GPL-3
license-file: LICENSE
build-type: Simple
stability: experimental
cabal-version: >= 1.10.0
tested-with: GHC == 7.10.3, GHC == 8.0.1
synopsis: Collection of alignment algorithms
description:
<http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming>
.
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.
Extra-Source-Files:
README.md
changelog.md
library
build-depends: base >= 4.7 && < 5.0
, containers >= 0.5
, fmlist >= 0.9
, vector >= 0.10
--
, ADPfusion == 0.5.2.*
, FormalGrammars == 0.3.1.*
, GrammarProducts == 0.1.1.*
, PrimitiveArray == 0.8.0.*
exposed-modules:
DP.HMM.States2
DP.Seq.Align.Global.Affine2
DP.Seq.Align.Global.Linear2
DP.Seq.Align.SemiGlobal.Infix2
DP.Tree.Align.Global.Affine2
DP.Tree.Align.Global.AffineSmall2
DP.Tree.Align.Global.Linear2
DP.Tree.Edit.Global.Linear2
default-language:
Haskell2010
default-extensions: BangPatterns
, FlexibleContexts
, FlexibleInstances
, MultiParamTypeClasses
, QuasiQuotes
, TemplateHaskell
, TypeFamilies
ghc-options:
-O2 -funbox-strict-fields
source-repository head
type: git
location: git://github.com/choener/AlignmentAlgorithms