Members of the Computational Biology Laboratory are involved in the development of various computational biology software packages, some of which are listed below.
Analysis of Protein Structure and Dynamics
Analyse domain movements in Proteins (DynDom).
The Determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
Analyse domain movements in large biomolecular complexes (DynDom3D).
Determine domains and hinge axes in large biomolecular complexes where two conformations are available.
Explore the biomolecular surface (Haptimol iSAS).
Search for water accessible channels and pockets in biomolecules using a haptic device.
Explore biomolecular flexibility (Haptimol ENM).
Use a haptic device to explore the mechanical properties of a biomolecule.
Predict protein function by comparing secondary structures (ZClass)
Takes input from a Protein Databank (PDB) file and converts it to a voxelised image which is can then be used to make rapid comparisons between different protein shapes.
Computational Biology of RNA
UEA sRNA workbench
The UEA sRNA workbench allows users to analyse next-generation sequencing short RNA data sets.
MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots).
MiRPlex is a tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input.
CCD is a Java software package for the selection of core collections of diverse taxa (e.g. from germplasm collections) that are intended to capture the genetic diversity of the input dataset.
CoMRiT is a software package written as a polymake extension to compute realisations of finite metric spaces.
FlatNJ (FlatNetJoining) is a program fro computing split networks that allow for interior vertices to be labelled while being (almost) planar.
Lasso is a heuristic for computing edge-weighted rooted (super)trees from partial distance data under the assumption that the distances satisfy the molecular clock assumption.
MY-CLOSURE is a Java program for computing a phylogenetic network from a collection of phylogenetic trees.
OSF-Builder is a Python program that allows to highlight potential introgression events occurring between lineages
Padre is a Java program for computing phylogenetic networks from rooted multi-labelled phylogenetic trees.
QNet is a software package written in Java for generating phylogenetic networks from quartet data.
Computing the block decomposition of a Quasi-median graph
SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees.
TriLoNet is a Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data.
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.
ViralNet is an application for estimating reticulated structures of mixed viral populations.
Matlab svm toolbox
This is a beta version of a MATLAB toolbox implementing Vapnik's support vector machine
Modelling Biological Systems
A package for modelling denitrification in bacteria
Population Structure Inference using Kernel-pca and Optimisation