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
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more...Analyse domain movements in large biomolecular complexes (DynDom3D)
DynDom -
more...Analyse domain movements in Proteins (DynDom)
The Determine domains, hinge axes and hinge bending residues in proteins where two conformations are available. -
more...Explore the biomolecular surface (Haptimol iSAS)
Search for water accessible channels and pockets in biomolecules using a haptic device. -
more...Explore biomolecular flexibility (Haptimol ENM).
Use a haptic device to explore the mechanical properties of a biomolecule. -
more...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
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more...sRNA
UEA Small RNA (sRNA) workbench allows users to analyse next-generation sequencing short RNA data sets. -
more...MIfold
MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots). -
more...miRPlex
MiRPlex is a tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input.
Phylogenetics
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more...CCD
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 -
more...CoMRiT
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 -
more...FlatNJ
FlatNJ (FlatNetJoining) is a program for computing split networks that allow for interior vertices to be labelled while being (almost) planar. -
more...Lasso
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. -
more...MY-CLOSURE
MY-CLOSURE is a Java program for computing a phylogenetic network from a collection of phylogenetic trees. -
more...OSF Builder
OSF-Builder is a Python program that allows to highlight potential introgression events occurring between lineages -
more...Padre
Padre is a Java program for computing phylogenetic networks from rooted multi-labelled phylogenetic trees -
more...QNet
QNet is a software package written in Java for generating phylogenetic networks from quartet data. -
more...QuasiDec
Computing the block decomposition of a Quasi-median graph -
more...Sprint
Calculate the minimal hybrid number and visualise a phylogenetic network with this minimum for a set of ploidy levels. -
more...SuperQ
SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees. -
more...TriLoNet
TriLoNet is a Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data. -
more...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. -
more...ViralNet
ViralNet is an application for estimating reticulated structures of mixed viral populations.
Conservation Biology
Others
