Members of the Computational Biology Laboratory are involved in the development of various computational biology software packages, some of which are listed below.
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AAMToolbox (Shape modelling Toolbox) For analysing populations of shapes and colours within the shapes using principal component analysis |
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CCD (Core collections of diverse taxa) 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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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. |
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Gftbox (Growth Toolbox) |
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HaptiMOL provides software enabling users to interact with molecules via haptic feedback devices. |
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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. |
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MY-CLOSURE MY-CLOSURE is a Java program implementing our approach for computing a phylogenetic network from a collection of phylogenetic trees which are not necessarily on the same but on overlapping taxa sets. Exploiting the fact that such a collection uniquely corresponds to a collection of partial splits, combinatorial rules are used by the program to associate a collection of full splits to the input collection of trees. This collection of splits can then be represented in the form of a phylogenetic network using the SplitsTree package. |
