Skip to content

Downloads


    Members of the Computational Biology Laboratory are involved in the development of various computational biology software packages, some of which are listed below.

  • Padre
    Padre is a Java program implementing our algorithm for computing a phylogenetic network from rooted a multi-labelled phylogenetic tree - provided in Newick format. Such trees are called multi-labelled because one or more of their leaves share the same label. Options are provided to move parts of the tree/network around the screen and perform the algorithm step by step. We plan to incorporate other complementary algorithms into this package in the future.
  • DynDom
    DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available. It uses a unique and rigorous methodology based in rigid-body kinematics, implemented in the DynDom program for the specific purpose of analysing movements in proteins in terms of the relative motions of quasi-rigid parts.
  • QTVolView
    Click here to download QTVolViewLITE a volume rendering package designed for optical projection tomography (OPT) data. Using hardware acceleration, it allows 256x256x256 voxel images to be displayed and manipulated in real-time. The data can represent multiple light channels.
  • AAMToolbox
    Click here to download AAMToolbox a Matlab toolbox with a Graphical User Interface for creating and viewing statistical shape and appearance models.
  • MIfold
    MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots). Given a sequence alignment MIfold computes and displays the mutual and sequence information of the alignment. MIfold also uses a dynamic programming algorithm to predict the secondary structure with maximal total mutual information.
  • Spectronet
    Spectronet is a package for the analysis and visualization of complex evolutionary data that is not best represented by a bifurcating tree. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allowing the user to interactively analyze the resulting collection using tools such as Lento-plots and median networks.
  • transsys
    The core of transsys is a computer language for describing regulatory gene networks in a comprehensive, object-oriented way. Based on such a description, gene expression dynamics can be simulated. The package modules for generating networks with pre-specified statistical properties, and for simulating gene expression measurements by microarrays. Finally, the integration of transsys with Lindenmayer-systems, called L-transsys, allows simulation of plant morphogenesis organised by regulatory networks.
  • VisRD
    VisRD is a software package allowing graphical inspection of the phylogenetic content of a sequence alignment, that is primarily intended for detection of recombination and recombination breakpoints. It is a quartet-based method, meaning that analysis is performed on quartets of sequences in the alignment. VisRD can utilize a variety of phylogeny estimation algorithms, of which statistical geometry has been most fully implemented.