FDK Software Library

FDK Software
AsVis - Visualization of association rules in SNP neighborhoods
A web application, available as source code, for visualizing association rules obtained from short, sequential data, such as SNP neighborhoods (on-line demo)
Blobber
A tool to extract all continuous volumes ("blobs") from density maps.
ContextPhone - Context-aware platform for mobile phones
ContextPhone is an open software platform for context-aware applications. It can be used to collect, analyse and transmit information about its context, as well as to tag and publish contextual media.
GESH - Geometric Pattern Matching in Three Dimensions
GESH applies geometric hashing to find protein structures from cryo-EM maps. It can be used to build a database of protein structures and query that database with EM-map and recognize proteins in that map.
HaploRec - Haplotype reconstruction
Scalable sofware for population-based haplotype phasing, especially for sparse marker maps.
HaploVisual - Haplotype Visualization
A web-based program for analyzing and visualizing haplotypes using small set of founder haplotypes.
HIT - a Haplotype Inference Technique
Software for haplotype reconstruction from a sample of genotypes (population-based haplotype phasing).
HPM and TreeDT - gene mapping methods
Software for association analysis, i.e., gene mapping based on linkage disequilibrium
Orient Express
A software system for determining relative orientations of cryo-electron images taken from random directions of identical objects using common lines techinques.
Sinogram denoiser
A program for denoising cryo-electron microscope images using sinograms.
Spade and Ethan
Tools for detection of spherical particles from electron micrographs
SUccinct Data Structures
Implementations of succinct data structures, especially of compressed full-text indexes. Includes a fully functional compressed suffix tree implementation, that can be used as a basis for implementing space-conscious versions of the numerous sequence analysis, information retrieval, pattern discovery, etc., algorithms based on suffix trees.
SYSFYS Software Releases
  • ReMatch - A tool for automating the biochemical nomenclature matching problem encountered in construction of metabolic network models
  • PIDC - Positional Isotopomer Distribution Calculator
    • Bassist - MCMC simulation for Bayesian statistical models
    Bassist is a tool that automates the use of hierarchical Bayesian models in complex analysis tasks, by generating a model-specific MCMC sampler.

    Pasi.Rastas@cs.Helsinki.FI