Software

• Phyre2 – Protein structure prediction server 
• SuSPect – Prediction of variant phenotype   
• PINALOG Alignment of interactomes
• CombFunc Protein Function Prediction
• 3DLigandSite an automated method for the prediction of ligand binding sites
• 3D Garden Global and Restrained Docking Exploration Nexus

• MMBGX - a tool to predict alternative splicing from Exon array data more accurately (publication)

• BSS Software Resources

Commercial Imaging Software bought with CISBIC funding (contact film-service@imperial.ac.uk)

• SimplePCI / HCImage (Hamamatsu) for image acquisition and analysis
• Autoquant (Mediacybernetics) for deconvolution
• Definiens XD (Definiens) for advanced image analysis

Commercial Data Analysis Software supported by the .

• Partek
• Genespring
• Ingenuity Pathway Analysis

Genome Visualisation (contact Derek Huntley)

• GEB (publication)

• Michael Stumpf Laboratory Software Tools

treespace  (on CRAN): Statistical Exploration of Landscapes of Phylogenetic Trees. Tools for the exploration of distributions of phylogenetic trees.

TransPhylo (with Xavier Didelot, hosted on his github): Reconstruction of transmission trees using genomic data.

treetop (on github): Label and compare topologies of (for now binary) rooted trees.

phybreak (with Don Klinkenburg in Holland, and Xavier Didelot ): Analysis of Outbreaks with Sequence Data. Implementation the outbreak analysis method described by Klinkenberg et al (2016) 

pySolo: a multi-platform software for sleep/activity analysis in Drosophila. pySolo aims at improving sharing – and communication – among researchers in the field ofsleep in invertebrates. Works with TriKinetics software.

ethoscope: The ethoscope platform is a collection of interconnected tools allowing biologists to design experiments, acquire and analyse a large amount of behavioural data. Provides a hardware and software solution.

rethomics: R package to study data from high-throughput animal behaviour monitoring