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ADPfusion
ADPfusion is a Haskell-based combinator library for efficient dynamic programming algorithms. We allow linear and context-free languages. The input domains can be strings, set, graphs, and other user-writeable types. Writing multi-context free grammars is possible as well. The algorithms are written in an embedded domain-specific language, directly within Haskell. This allows us to make use of the full language at any time.
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ADPfusionForest
ADPfusionForest extends the ADPfusion dynamic programming framework with capabilities for algorithms operating on trees and forests.
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ADPfusionPSCFG
ADPfusionPSCFG extends the ADPfusion dynamic programming framework with capabilities for Infernal Covariance models
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ADPfusionSet
ADPfusionSet extends the ADPfusion dynamic programming framework with capabilities for set-based algorithms
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ADPfusionSubword
ADPfusionSubword extends the ADPfusion dynamic programming framework with capabilities for context-free grammars on strings.
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AlignmentAlgorithms
A small collection of formal grammars for alignment-style problems.
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BenchmarkHistory
Benchmark whole programs with performance history.
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BiobaseBlast
todo
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BiobaseENA
European Nucleotide Archive data
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BiobaseFasta
todo
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BiobaseInfernal
Infernal and HMMer data structures and tools
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BiobaseMAF
todo
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BiobaseNewick
todo
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BiobaseTurner
todo
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BiobaseTypes
Basic types used in bioinformatics
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BiobaseXNA
RNA, DNA, amino acid sequence representations
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CMCompare Webserver
Webserver to facilitate the computation of RNA family model similarity.
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CMCompare
Compute the similarity between two RNA families via their covariance models. The result is the link score, which measures similarity, together with a link sequence, which provides the best-matching sequence for both models. High-scoring models are not well separated. In such a case, one might investigate in potential biological similarities, or possibly misconstructed families.
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CMhistogram
todo
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DPutils
small set of utility functions (mostly for DP)
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DnaProteinAlignment
Alignment of DNA and protein sequences in the presence of insertion/deletion editing.
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ForestStructures
todo
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Forestry
todo
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FormalGrammars
An improved embedded domain-specific language for formal grammars on top of ADPfusion. This library abstracts away the underlying ADPfusion syntax and provides a more pleasent environment for language design.
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Gene-CluEDO
Gene Cluster Evolution Determined Order
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GenussFold
A simple pseudoknotted RNA folding grammar. This application mostly serves as an example for the creation of multi-context-free grammars in ADPfusion, and FormalGrammars.
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GrammarProducts
Grammar products lift algebraic operations to the level of formal grammars. We can now add, subtract, and most importantly multiply, formal grammars with each other. This considerably simplifies the design of novel algorithms. We provide a number of examples.
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HeraldicAnnotations
todo
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HeraldicGlossary
todo
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InternedData
todo
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LinguisticsTypes
Basic types for natural language processing (NLP).
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MutationOrder
Most likely order of mutation events in RNA
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NaturalLanguageAlphabets
Simple scoring system for alignments of words in natural languages.
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OrderedBits
Efficient ordered (by population count) enumeration of Ints.
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PrimitiveArray-Pretty
Prettyprinting of posterior probability information contained in primitive arrays. Currently more general in that we just process lists of values.
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PrimitiveArray
This library provides low-level functionality for memoization in ADPfusion. The arrays provided with this library are also well-suited for multi-dimensional arrays of raw data.
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ProfileSCFGs
Profile Stochastic Context-free grammars
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RNAdesign
The RNAdesign program allows us to specify one or more secondary structure and an optimization function. It then generates RNA sequences that have the given secondary structure(s) as low-energy structures. A prototypical application is RNA riboswitch design.
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RNAdraw
todo
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RNAwolf
todo
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SciBaseTypes
Science/humanities base types
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ShortestPathProblems
Generic solutions for Travelling Salesman and Hamiltonian Path problems
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SimulateGeneDuplications
Simulation of evolutionary gene cluster divergence.
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SuffixStructures
todo
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ViennaRNA-bindings
Bindings to the Vienna RNA secondary structure prediction library
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ViennaRNA-extras
todo
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WienRNA
todo
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WordAlignment
Bigram word pair alignments for linguistics.
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bimaps
Bijections
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fgl-extras-decompositions
Graph ear decompositions for the fgl.