A showcase of the computational biology software packages A showcase of the computational biology software packages

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

DynDom logoAnalyse domain movements in Proteins (DynDom).
The Determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
 

DynDom3DAnalyse domain movements in large biomolecular complexes (DynDom3D).
Determine domains and hinge axes in large biomolecular complexes where two conformations are available.
 

Haptimol iSASExplore the biomolecular surface (Haptimol iSAS). 
Search for water accessible channels and pockets in biomolecules using a haptic device.

 

Haptimol ENMExplore biomolecular flexibility (Haptimol ENM). 
Use a haptic device to explore the mechanical properties of a biomolecule.

 

ZClassPredict 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

sRNAUEA sRNA workbench
The UEA sRNA workbench allows users to analyse next-generation sequencing short RNA data sets.


MIfold

MIfold
MIfold is a matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots).

miRPlex

miRPlex 
MiRPlex is a tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input.

 

Modelling and Analysis of Biological Growth (Bangham Lab)

AAMT ToolboxAnalyse shapes in 2D and 3D images, petals, leaves and faces (AAMToolbox). 
The AAMToolbox enables the user analyse the shape and colour of collections of similar objects.

 

GFtboxModel growth of organs and tissue (GFtbox) 
GFtbox is an implementation of the Growing Polarised Tissue Framework for understanding and modelling relationships between gene activity and growth of shapes.
 

Sector Analysis ToolboxAnalyse marked clones and warp organ shape (Sector Analysis Toolbox)
The AAMToolbox enables the user analyse the shape and colour of collections of similar objects.
 


VolviewerHigh speed view and quantify 3D solid images, png stacks and OMERO (Volviewer)
VolViewer uses OpenGL and Qt to provide a user friendly application to interactively explore and quantify multi-dimensional biological images.


Phylogenetics

CCD logoCCD
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 logoCoMRiT
CoMRiT is a software package written as a polymake extension to compute realisations of finite metric spaces.


FlatNJFlatNJ
FlatNJ (FlatNetJoining) is a program fro computing split networks that allow for interior vertices to be labelled while being (almost) planar.
 

Lasso thumbnailLasso
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-ClosureMy-Closure
MY-CLOSURE is a Java program for computing a phylogenetic network from a collection of phylogenetic trees.
 

Padre logoPadre
Padre is a Java program for computing phylogenetic networks from rooted multi-labelled phylogenetic trees.
 

QNet logoQNet
QNet is a software package written in Java for generating phylogenetic networks from quartet data.

 

QuaisDec logoQuasiDec
Computing the block decomposition of a Quasi-median graph

 

SuperQ logoSuperQ
SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees.

 

Trilonet logoTriLoNet
TriLoNet is a Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data.
 

VisRDVisRD
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.

 

VirNet iconViralNet
ViralNet is an application for estimating reticulated structures of mixed viral populations.

 

Conservation Biology

Specsel logoSpecsel
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.


Matlab

Matlab SVM toolboxMatlab svm toolbox
This is a beta version of a MATLAB toolbox implementing Vapnik's support vector machine


 

Modelling Biological Systems

Modelling denitrificationModelling Denitrification
A package for modelling denitrification in bacteria

 

Population Genetics

Psiko iconPsiko
Population Structure Inference using Kernel-pca and Optimisation