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  • ADPfusion


    Build Status

    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.


  • ADPfusionForest


    Build Status

    ADPfusionForest extends the ADPfusion dynamic programming framework with capabilities for algorithms operating on trees and forests.


  • ADPfusionPSCFG


    Build Status

    ADPfusionPSCFG extends the ADPfusion dynamic programming framework with capabilities for Infernal Covariance models


  • ADPfusionSet


    Build Status

    ADPfusionSet extends the ADPfusion dynamic programming framework with capabilities for set-based algorithms


  • ADPfusionSubword


    Build Status

    ADPfusionSubword extends the ADPfusion dynamic programming framework with capabilities for context-free grammars on strings.


  • AlignmentAlgorithms


    Build Status

    A small collection of formal grammars for alignment-style problems.


  • BenchmarkHistory


    Build Status

    Benchmark whole programs with performance history.


  • BiobaseBlast


    Build Status

    todo


  • BiobaseENA


    Build Status

    European Nucleotide Archive data


  • BiobaseFasta


    Build Status

    todo


  • BiobaseInfernal


    Build Status

    Infernal and HMMer data structures and tools


  • BiobaseMAF


    Build Status

    todo


  • BiobaseNewick


    Build Status

    todo


  • BiobaseTurner


    Build Status

    todo


  • BiobaseTypes


    Build Status

    Basic types used in bioinformatics


  • BiobaseXNA


    Build Status

    RNA, DNA, amino acid sequence representations


  • CMCompare Webserver

    Webserver to facilitate the computation of RNA family model similarity.


  • CMCompare


    Build Status

    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.


  • CMhistogram


    Build Status

    todo


  • DPutils


    Build Status

    small set of utility functions (mostly for DP)


  • DnaProteinAlignment


    Build Status

    Alignment of DNA and protein sequences in the presence of insertion/deletion editing.


  • ForestStructures


    Build Status

    todo


  • Forestry


    Build Status

    todo


  • FormalGrammars


    Build Status

    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.


  • Gene-CluEDO


    Build Status

    Gene Cluster Evolution Determined Order


  • GenussFold


    Build Status

    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.


  • GrammarProducts


    Build Status

    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.


  • HeraldicAnnotations


    Build Status

    todo


  • HeraldicGlossary


    Build Status

    todo


  • InternedData


    Build Status

    todo


  • LinguisticsTypes


    Build Status

    Basic types for natural language processing (NLP).


  • MutationOrder


    Build Status

    Most likely order of mutation events in RNA


  • NaturalLanguageAlphabets


    Build Status

    Simple scoring system for alignments of words in natural languages.


  • OrderedBits


    Build Status

    Efficient ordered (by population count) enumeration of Ints.


  • PrimitiveArray-Pretty


    Build Status

    Prettyprinting of posterior probability information contained in primitive arrays. Currently more general in that we just process lists of values.


  • PrimitiveArray


    Build Status

    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.


  • ProfileSCFGs


    Build Status

    Profile Stochastic Context-free grammars


  • RNAdesign


    Build Status

    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.


  • RNAdraw


    Build Status

    todo


  • RNAwolf


    Build Status

    todo


  • SciBaseTypes


    Build Status

    Science/humanities base types


  • ShortestPathProblems


    Build Status

    Generic solutions for Travelling Salesman and Hamiltonian Path problems


  • SimulateGeneDuplications


    Build Status

    Simulation of evolutionary gene cluster divergence.


  • SuffixStructures


    Build Status

    todo


  • ViennaRNA-bindings


    Build Status

    Bindings to the Vienna RNA secondary structure prediction library


  • ViennaRNA-extras


    Build Status

    todo


  • WienRNA


    Build Status

    todo


  • WordAlignment


    Build Status

    Bigram word pair alignments for linguistics.


  • bimaps


    Build Status

    Bijections


  • fgl-extras-decompositions


    Build Status

    Graph ear decompositions for the fgl.