Software



Resampling in Lisp




a domain-specific language (DSL) for statistical tests of arbitrary S-expressions (and more)
Source code (tar.gz)

DOCKTITE

Efficient, reliable covalent docking in Molecular Operating Environment (MOE)

SVL-Source-Code at MOE repository
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J. Chem. Inf. Model., accepted, 2014



libTransferEntropy

Compute transfer entropy (including statistical permutation test) for time series Frontiers in Physics 3(2015)10

BioPhysConnectoR

Molecular (Co)evolution and Biophysical/Molecular Dynamics in R;
uses Information Theory, Elastic Network Models, Multi-Core Computations etc.

Code at CRAN
Our BioPhysConnectoR-Website
BMC Bioinformatics 2010, 11:199

CoMIC - Coevolution via MI on CUDA

We've implemented a massively-parallel version of our normalization procedure for mutual information values in molecular (co)evolution. To this end we compute replica-wise Z-scores and percentiles of a parameter-free model of neutral evolution.
CoMIC-Website

ViPhy

Visual Analytics for Phylogenies

ViPhy-Website


IEEE Conference on Visual Analytics Science and Technology (VAST2011), 31-40, 2011

MatrixVis

Visual Analytics for (Co)evolutionary Matrices

MatrixVis-Website

BMC Bioinformatics, 11:330, 2010