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phylocomgraph.cabal
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name: phylocomgraph
version: 0.0.1.0
-- A short (one-line) description of the package.
-- synopsis:
-- A longer description of the package.
-- description:
license: BSD3
license-file: LICENSE
author: Ward Wheeler
maintainer: wheeler@amnh.org
-- A copyright notice.
-- copyright:
category: Biology
build-type: Simple
extra-source-files: README.md
cabal-version: >= 1.22
flag build-cpp-files
description: Toggles the C++ files being successfully build.
default: True
library
other-extensions: MonadFailDesugaring
build-depends: base >=4.8
, bimap
, blaze-html
, case-insensitive
-- >=0.5.8 Required for Data.Map.restrictKeys
, containers >=0.5.8
, deepseq
, dlist
, graphviz
, hashable
, hashtables
, integer-gmp
, keys
, lens
, mono-traversable >=1.0
, mtl
, parallel
, pcg-file-parsers
, pcg-utility
, pointed
, pretty-tree
, primitive
, QuickCheck
, scientific
, semigroupoids
, semigroups
, text
, transformers
, unordered-containers
, vector
-- >=3.4 required for corrected definition of (!) & index
, vector-instances >=3.4
, xml
default-language: Haskell2010
ghc-options: -O2
-g
-- -debug -optl-static
-- Sanity check warnings
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: src, ffi
-- ld-options: -lstdc++
extra-libraries: stdc++
if flag(build-cpp-files)
cc-options: --std=c++11 -g
else
cc-options: --std=c11
-pedantic
-Wall -Wextra
-fPIC
-- We must provide the full relative path to every C file that the project depends on.
c-sources:
-- ffi/Analysis/Parsimony/Binary/SequentialAlign/sequentialAlign.c
-- ffi/Analysis/Parsimony/Binary/SequentialAlign/dynamicCharacterOperations.c
ffi/external_direct_optimization/c_alignment_interface.c
ffi/external_direct_optimization/c_code_alloc_setup.c
ffi/external_direct_optimization/costMatrix.c
ffi/external_direct_optimization/alignmentMatrices.c
ffi/external_direct_optimization/dyn_character.c
ffi/external_direct_optimization/alignCharacters.c
ffi/external_direct_optimization/ukkCheckPoint.c
ffi/external_direct_optimization/ukkCommon.c
-- ffi/memoized_tcm/dynamicCharacterOperations.h
ffi/memoized_tcm/dynamicCharacterOperations.c
-- ffi/memoized_tcm/costMatrix.h
ffi/memoized_tcm/costMatrix.cpp
-- ffi/memoized_tcm/costMatrixWrapper.h
ffi/memoized_tcm/costMatrixWrapper.c
-- ffi/sequential_align/sequentialAlignInterface.h
ffi/sequential_align/sequentialAlignInterface.c
-- ffi/sequential_align/sequentialAlign.h
ffi/sequential_align/sequentialAlign.c
-- ffi/sequential_align/sequentialAlignOutputTypes.h
-- Here we list all directories that contain C header files that the FFI tools will need
-- to locate when preprocessing the C files. Without listing the directories containing
-- the C header files here, the FFI preprocession (hsc2hs, c2hs,etc.) will fail to locate
-- the requisite files.
-- Note also, that the parent directory of the nessicary C header files must be specified.
-- The preprocesser will not recursively look in subdirectories for C header files!
include-dirs:
ffi/external_direct_optimization
ffi/memoized_tcm
ffi/sequential_align
-- Modules exported by the library.
exposed-modules:
-- Analysis.ImpliedAlignment
Analysis.Parsimony.Additive.Internal
Analysis.Parsimony.Dynamic.DirectOptimization
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise
Analysis.Parsimony.Dynamic.SequentialAlign
Analysis.Parsimony.Fitch.Internal
Analysis.Parsimony.Sankoff.Internal
Analysis.Scoring
Bio.Character
Bio.Character.Decoration.Additive
Bio.Character.Decoration.Continuous
Bio.Character.Decoration.Discrete
Bio.Character.Decoration.Dynamic
Bio.Character.Decoration.Fitch
Bio.Character.Decoration.Metric
Bio.Character.Decoration.NonMetric
Bio.Character.Encodable
Bio.Character.Encodable.Continuous
Bio.Character.Exportable
Bio.Character.Parsed
Bio.Metadata
Bio.Metadata.CharacterName
Bio.Metadata.Continuous
Bio.Metadata.Discrete
Bio.Metadata.DiscreteWithTCM
Bio.Metadata.Dynamic
Bio.Metadata.Parsed
Bio.Sequence
Bio.Sequence.Block
Bio.Graph
Bio.Graph.Component
Bio.Graph.Forest.Parsed
Bio.Graph.LeafSet
Bio.Graph.Node
Bio.Graph.PhylogeneticDAG
Bio.Graph.ReferenceDAG
Bio.Graph.ReferenceDAG.Internal
Bio.Graph.Solution
Bio.Graph.ZipperDAG
Control.Evaluation
Control.Parallel.Custom
Control.Monad.Logger
Data.Alphabet
Data.Alphabet.IUPAC
Data.EdgeLength
Data.TCM
Data.TCM.Memoized
Data.TopologyRepresentation
-- Text.HTML.Class
-- Text.HTML.Custom
Text.Newick.Class
Text.XML
Text.XML.Custom
-- probably can be moved to other-modules:
Test.Custom.NucleotideSequence
Test.Custom.DynamicCharacterNode
other-modules:
Analysis.Parsimony.Dynamic.DirectOptimization.DeletionEvents
Analysis.Parsimony.Dynamic.DirectOptimization.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.InsertionEvents
Analysis.Parsimony.Dynamic.DirectOptimization.InsertionEvents.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.FFI
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.NeedlemanWunsch
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen.Ribbon
Analysis.Parsimony.Dynamic.SequentialAlign.FFI
Bio.Character.Decoration.Additive.Class
Bio.Character.Decoration.Additive.Internal
Bio.Character.Decoration.Continuous.Class
Bio.Character.Decoration.Continuous.Internal
Bio.Character.Decoration.Dynamic.Class
Bio.Character.Decoration.Dynamic.Internal
Bio.Character.Decoration.Fitch.Class
Bio.Character.Decoration.Fitch.Internal
Bio.Character.Decoration.Metric.Class
Bio.Character.Decoration.Metric.Internal
Bio.Character.Decoration.NonMetric.Class
Bio.Character.Decoration.NonMetric.Internal
Bio.Character.Decoration.Shared
Bio.Character.Encodable.Continuous.Class
Bio.Character.Encodable.Continuous.Internal
Bio.Character.Encodable.Dynamic
Bio.Character.Encodable.Dynamic.Class
Bio.Character.Encodable.Dynamic.Internal
Bio.Character.Encodable.Internal
Bio.Character.Encodable.Static
Bio.Character.Encodable.Static.Class
Bio.Character.Encodable.Static.Internal
Bio.Character.Encodable.Stream
Bio.Character.Exportable.Class
Bio.Character.Parsed.Class
Bio.Character.Parsed.Internal
Bio.Metadata.General
Bio.Metadata.General.Class
Bio.Metadata.General.Internal
Bio.Metadata.Discrete.Class
Bio.Metadata.Discrete.Internal
Bio.Metadata.DiscreteWithTCM.Class
Bio.Metadata.DiscreteWithTCM.Internal
Bio.Metadata.Dynamic.Class
Bio.Metadata.Dynamic.Internal
Bio.Graph.Constructions
Bio.Graph.Forest
Bio.Graph.Node.Class
Bio.Graph.Node.Internal
Bio.Graph.PhylogeneticDAG.Class
Bio.Graph.PhylogeneticDAG.Internal
Bio.Graph.PhylogeneticDAG.NetworkEdgeQuantification
Bio.Graph.PhylogeneticDAG.DynamicCharacterRerooting
Bio.Graph.PhylogeneticDAG.Postorder
Bio.Graph.PhylogeneticDAG.Preorder
Bio.Graph.PhylogeneticDAG.Reification
Bio.Graph.PhylogeneticDAG.TotalEdgeCost
Bio.Graph.ZipperDAG.Internal
Bio.Sequence.Internal
Bio.Sequence.Block.Builder
Bio.Sequence.Block.Internal
Control.Evaluation.Unit
Control.Evaluation.Internal
Control.Evaluation.Trans
Data.Alphabet.Internal
Data.EdgeSet
Data.Range
Data.TCM.Internal
Data.TCM.Memoized.FFI
Data.Vector.NonEmpty
Test.QuickCheck.Arbitrary.Instances
Text.XML.Class
executable pcg
main-is: Main.hs
build-depends: phylocomgraph
, base >=4.8
, blaze-html
-- Required for Data.Map.restrictKeys
, containers >=0.5.8
, deepseq
, directory
, Glob
, graphviz
, hashable
, keys
, lens
, megaparsec >=5.0
, mono-traversable >=1.0
, parallel
, pcg-file-parsers
, pcg-language
, pcg-utility
, primitive
, random-shuffle
, semigroupoids
, semigroups
, text
, time
, transformers
, vector
, vector-instances >=3.4
, xml
default-language: Haskell2010
ghc-options: -O2
-g
-- This is to enable thread parralellism at compile time
-threaded
-- -rtsopts -with-rtsopts=-N8
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: app
other-modules:
PCG.Command.Build.Evaluate
PCG.Command.Read.DecorationInitialization
PCG.Command.Read.Evaluate
PCG.Command.Read.ReadError
PCG.Command.Read.Unification.Master
PCG.Command.Read.Unification.UnificationError
-- PCG.Command.Report.CharacterMatrix
PCG.Command.Report.DynamicCharacterTable
PCG.Command.Report.Evaluate
PCG.Command.Report.GraphViz
-- PCG.Command.Report.ImpliedAlignmentFasta
-- PCG.Command.Report.Internal
-- PCG.Command.Report.Metadata
-- PCG.Command.Report.TaxonMatrix
-- PCG.Command.Report.Newick
-- PCG.Command.Report.Validate
PCG.Computation.Internal
executable fasta-differ
main-is: fasta-differ.hs
build-depends: phylocomgraph
, base >=4.8
, containers
, pcg-file-parsers
, keys
, megaparsec >=5.0
default-language: Haskell2010
ghc-options: -O2
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: utils
executable 2d-do-comparison
main-is: 2d-do-comparison.hs
build-depends: phylocomgraph
, base >=4.8
, bimap
, QuickCheck
default-language: Haskell2010
ghc-options: -O2
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: utils
executable 3d-do-comparison
main-is: 3d-do-comparison.hs
build-depends: phylocomgraph
, base >=4.8
, bimap
, deepseq
, QuickCheck
default-language: Haskell2010
ghc-options: -O2
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: utils
executable affine-safety
main-is: affine-safety.hs
build-depends: phylocomgraph
, base >=4.8
, bimap
, QuickCheck
default-language: Haskell2010
ghc-options: -O2
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: utils
executable sequential-alignment-invariants
main-is: sequential-alignment-invariants.hs
build-depends: phylocomgraph
, base >=4.8
, bimap
, QuickCheck
default-language: Haskell2010
ghc-options: -O2
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: utils
executable three-way-mean-check
main-is: three-way-mean-check.hs
build-depends: phylocomgraph
, base >=4.8
, bimap
, lens
, QuickCheck
default-language: Haskell2010
ghc-options: -O2
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: utils
executable ukkonen-do-comparison
main-is: ukkonen-do-comparison.hs
build-depends: phylocomgraph
, base >=4.8
, bimap
, QuickCheck
default-language: Haskell2010
ghc-options: -O2
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
hs-source-dirs: utils
Test-Suite testsuite
type: exitcode-stdio-1.0
main-is: TestAll.hs
build-depends: base >=4.8
, bimap
, blaze-html
, case-insensitive
-- >=0.5.8 Required for Data.Map.restrictKeys
, containers >=0.5.8
, deepseq
, dlist
, either
, graphviz
, hashable
, hashtables
, integer-gmp
, keys
, lens
, mono-traversable >=1.0
, mtl
, parallel
, pcg-file-parsers
, pcg-utility
, pointed
, pretty-tree
, primitive
, QuickCheck
, quickcheck-properties
, scientific
, semigroupoids
-- required for Data.Semigroup.Foldable.toNonEmpty
, semigroups >=5.2.1
, split
, tasty
, tasty-hunit
, tasty-quickcheck
, tasty-smallcheck
, text
, time
, transformers
, unordered-containers
, vector
-- >=3.4 required for corrected definition of (!) & index
, vector-instances >=3.4
, xml
-- build-depends: base >=4.8
-- , bimap
-- , bv
-- , containers >=0.5.8
-- , deepseq
-- , directory
-- , dlist
-- , hashable
-- , either
-- , keys
-- , lens
-- , matrix
-- , megaparsec >=5.0
-- , mtl
-- , mono-traversable >=1.0
-- , parallel
-- , phylocomgraph
-- , pcg-utility
-- , safe
-- , scientific
-- , semigroupoids
-- , semigroups
-- , smallcheck
-- , text
-- , transformers
-- , unordered-containers
-- , vector
-- , vector-instances
-- , xml
default-language: Haskell2010
hs-source-dirs: test, src, app, ffi
extra-libraries: stdc++
if flag(build-cpp-files)
cc-options: --std=c++11 -g
else
cc-options: --std=c11
-- We must provide the full relative path to every C file that the project depends on.
c-sources:
-- ffi/Analysis/Parsimony/Binary/SequentialAlign/sequentialAlign.c
-- ffi/Analysis/Parsimony/Binary/SequentialAlign/dynamicCharacterOperations.c
ffi/external_direct_optimization/c_alignment_interface.c
ffi/external_direct_optimization/c_code_alloc_setup.c
ffi/external_direct_optimization/costMatrix.c
ffi/external_direct_optimization/alignmentMatrices.c
ffi/external_direct_optimization/dyn_character.c
ffi/external_direct_optimization/alignCharacters.c
ffi/external_direct_optimization/ukkCheckPoint.c
ffi/external_direct_optimization/ukkCommon.c
-- ffi/memoized_tcm/dynamicCharacterOperations.h
ffi/memoized_tcm/dynamicCharacterOperations.c
-- ffi/memoized_tcm/costMatrix.h
ffi/memoized_tcm/costMatrix.cpp
-- ffi/memoized_tcm/costMatrixWrapper.h
ffi/memoized_tcm/costMatrixWrapper.c
-- ffi/sequential_align/sequentialAlignInterface.h
ffi/sequential_align/sequentialAlignInterface.c
-- ffi/sequential_align/sequentialAlign.h
ffi/sequential_align/sequentialAlign.c
-- ffi/sequential_align/sequentialAlignOutputTypes.h
-- Here we list all directories that contain C header files that the FFI tools will need
-- to locate when preprocessing the C files. Without listing the directories containing
-- the C header files here, the FFI preprocession (hsc2hs, c2hs,etc.) will fail to locate
-- the requisite files.
-- Note also, that the parent directory of the nessicary C header files must be specified.
-- The preprocesser will not recursively look in subdirectories for C header files!
include-dirs:
ffi/external_direct_optimization
ffi/memoized_tcm
ffi/sequential_align
ghc-options: -O2
-threaded
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monadfail-instances
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
other-modules:
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.FFI
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.NeedlemanWunsch
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Test
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen.Ribbon
Bio.Character
Bio.Character.Encodable
Bio.Character.Encodable.Continuous
Bio.Character.Encodable.Continuous.Class
Bio.Character.Encodable.Continuous.Internal
Bio.Character.Encodable.Dynamic
Bio.Character.Encodable.Dynamic.Class
Bio.Character.Encodable.Dynamic.Internal
Bio.Character.Encodable.Dynamic.Test
Bio.Character.Encodable.Static
Bio.Character.Encodable.Static.Class
Bio.Character.Encodable.Static.Internal
Bio.Character.Encodable.Static.Test
Bio.Character.Encodable.Internal
Bio.Character.Encodable.Static
Bio.Character.Encodable.Static.Class
Bio.Character.Encodable.Static.Internal
Bio.Character.Encodable.Stream
Bio.Character.Exportable
Bio.Character.Exportable.Class
Bio.Character.Parsed
Bio.Character.Parsed.Class
Bio.Character.Parsed.Internal
Bio.Metadata
Bio.Metadata.Parsed
Control.Evaluation.Internal
Control.Evaluation.Test
Control.Evaluation.Unit
Control.Monad.Logger
Data.Alphabet
Data.Alphabet.IUPAC
Data.Alphabet.Internal
Data.Range
Data.TCM
Data.TCM.Memoized
Data.TCM.Memoized.FFI
Data.TCM.Internal
Data.Vector.NonEmpty
Test.QuickCheck.Arbitrary.Instances
Test.Custom.NucleotideSequence
TestSuite.ExecutableTests
TestSuite.LibraryTests
Text.XML
Text.XML.Class
Text.XML.Custom
-- Analysis.ImpliedAlignment.AlignmentContext
-- Analysis.ImpliedAlignment.DynamicProgramming
-- Analysis.ImpliedAlignment.Internal
-- Analysis.ImpliedAlignment.Standard
-- Analysis.ImpliedAlignment.Test
-- Analysis.ImpliedAlignment.Test.Trees
-- Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Internal
-- Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Test
---- Analysis.Parsimony.Binary.Internal
---- Analysis.Parsimony.Binary.Test
-- Analysis.Parsimony.Dynamic.DirectOptimization.DeletionEvents
-- Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise
-- Analysis.Parsimony.Dynamic.DirectOptimization.InsertionEvents
-- Analysis.Parsimony.Dynamic.DirectOptimization.InsertionEvents.Internal
-- Analysis.Parsimony.Dynamic.DirectOptimization.InsertionEvents.Test
---- Analysis.Parsimony.Binary.Fitch
-- Bio.Character
-- Bio.Character.Decoration.Additive
-- --Bio.Character.Decoration.Continuous
-- Bio.Character.Decoration.Discrete
-- Bio.Character.Decoration.Dynamic
-- Bio.Character.Decoration.Fitch
-- Bio.Character.Decoration.Metric
-- Bio.Character.Decoration.NonMetric
-- Bio.Character.Encodable
-- Bio.Character.Exportable.Class
-- Bio.Character.Parsed
-- Bio.Character.Decoration.Additive.Class
-- Bio.Character.Decoration.Additive.Internal
-- --Bio.Character.Decoration.Continuous.Class
-- --Bio.Character.Decoration.Continuous.Internal
-- Bio.Character.Decoration.Dynamic.Class
-- Bio.Character.Decoration.Dynamic.Internal
-- Bio.Character.Decoration.Fitch.Class
-- Bio.Character.Decoration.Fitch.Internal
-- Bio.Character.Decoration.Metric.Class
-- Bio.Character.Decoration.Metric.Internal
-- Bio.Character.Decoration.NonMetric.Class
-- Bio.Character.Decoration.NonMetric.Internal
-- Bio.Character.Encodable.Dynamic
-- Bio.Character.Encodable.Dynamic.Class
-- Bio.Character.Encodable.Dynamic.Internal
-- Bio.Character.Encodable.Internal
-- Bio.Character.Encodable.Static
-- Bio.Character.Encodable.Static.Class
-- Bio.Character.Encodable.Static.Internal
-- Bio.Character.Encodable.Stream
-- Bio.Character.Parsed.Class
-- Bio.Character.Parsed.Internal
-- Bio.Metadata
-- Bio.Metadata.CharacterName
-- --Bio.Metadata.Continuous
-- Bio.Metadata.Discrete
-- Bio.Metadata.Parsed
-- Bio.Metadata.General
-- Bio.Metadata.General.Class
-- Bio.Metadata.General.Internal
-- Bio.Metadata.Discrete.Class
-- Bio.Metadata.Discrete.Internal
-- Bio.Sequence
-- Bio.Sequence.Block
-- Bio.Graph
-- Bio.Graph.Component
-- Bio.Graph.LeafSet
-- Bio.Graph.Node
-- Bio.Graph.ReferenceDAG
-- Bio.Graph.ZipperDAG
-- Bio.Graph.Forest
-- Bio.Graph.ReferenceDAG.Internal
-- Bio.Graph.ZipperDAG.Internal
-- Bio.Sequence.Internal
--
--
--
-- Control.Evaluation.Internal
-- Control.Evaluation.Test
-- Control.Evaluation.Unit
-- Data.Alphabet.IUPAC
-- Data.BitMatrix.Internal
-- Data.BitMatrix.Test