TBI Software Page


  NOTE: Please read the copyright notices included in the packages below. It's not the same for all of them!
  • The Vienna RNA Package for predicting and comparing RNA Secondary Structures
    Interactive access:
  • The RNA secondary structure prediction server for single sequences.
  • The Alifold server for predicting consensus structures from an alignment
  • The RNA sequence design server

  • Alignments of Nucleic Acid Sequences
    with the codaln/code2aln program, which uses information on coding regions to improve the alignment.

  • Detecting Conserved RNA Structures
    with the alidot/pfrali software for extracting conserved RNA secondary structure elements from a combination of sequence alignment and structure prediction.

  • Kinetic folding of RNA
    The program kinfold

  • Basin Structure of Landscapes
    The program barriers

  • The ToyChem Package is a computational toolkit implementing an artificial chemistry model which has a built in thermodynamics. Molecules and reactions are modeled as graphs and graph transformations respectively. Physico-chemical properties of molecules are calculated directly from the molecular graphs and are consistent within the ToyChemistry universe (currently not available for download).

  • The Graph Grammar Library (GGL) is an C++ library (based on the Boost Graph Library) to handle graph transformation. The library is geared towards chemical graph transformations and can be used to algebraically expand chemical reaction networks. The includes the functionallity of the ToyChem Package.

  • Set-theoretical operations for chemical reaction networks
    The Vienna Reaction Network Library (Vienna-RNL)

  • Integrator for SBML Models
    The program SBML_odeSolver

  • Relevant Cycles of undirected graphs
    The program cycdeco

  • Walter Fontana's AlChemy related software

  • Jan Cupal's WinTeX TeX editor and shell for Windows 3.1 and Win95

  • The ProbA program for stochastic pairwise sequence alignments, including calculation of the partition function and match probabilities.

  • Our anonymous FTP-server contains mostly prehistoric stuff
    • Ivo L. Hofacker, <ivo@tbi.univie.ac.at>
    Last modified: 2010-01-28 00:24:28 xtof