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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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Analyse domain movements in Proteins (DynDom)
more...The Determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
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Explore the biomolecular surface (Haptimol iSAS)
more...Search for water accessible channels and pockets in biomolecules using a haptic device.
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Explore biomolecular flexibility (Haptimol ENM).
more...Use a haptic device to explore the mechanical properties of a biomolecule.
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Predict protein function by comparing secondary structures (ZClass)
more...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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sRNA
more...UEA Small RNA (sRNA) workbench allows users to analyse next-generation sequencing short RNA data sets.
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MIfold
more...MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots).
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miRPlex
more...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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CCD
more...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
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CoMRiT
more...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
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FlatNJ
more...FlatNJ (FlatNetJoining) is a program for computing split networks that allow for interior vertices to be labelled while being (almost) planar.
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Lasso
more...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.
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MY-CLOSURE
more...MY-CLOSURE is a Java program for computing a phylogenetic network from a collection of phylogenetic trees.
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OSF Builder
more...OSF-Builder is a Python program that allows to highlight potential introgression events occurring between lineages
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Padre
more...Padre is a Java program for computing phylogenetic networks from rooted multi-labelled phylogenetic trees
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QNet
more...QNet is a software package written in Java for generating phylogenetic networks from quartet data.
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Sprint
more...Calculate the minimal hybrid number and visualise a phylogenetic network with this minimum for a set of ploidy levels.
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SuperQ
more...SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees.
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TriLoNet
more...TriLoNet is a Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data.
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VisRD
more...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.
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ViralNet
more...ViralNet is an application for estimating reticulated structures of mixed viral populations.
Conservation Biology
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Specsel
more...SpecSel, (Species Selection), is a program written in Java which computes a set of indicator species from a pool of candidate species using an objective niche-based approach.
Others
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Matlab SVM Toolbox
more...This is a beta version of a MATLAB toolbox implementing Vapnik's support vector machine
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