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Download Bioinformatics Software

ALICAO - Contact-based Sequence Alignment Program: zipped archive; extract with 'unzip' Program to generate contact map from (single chain) PDB file: zipped binary; extract with 'unzip' Example: zipped archive; extract with 'unzip'

ALISS - Unified Sequence and Structure Alignment Program and examples: zipped archive; extract with 'unzip'

CAO contact substitution matrices
CAO50   CAO80   CAO100   CAO120   CAO200
Example implementation of CAO80

Metabolic Flux Estimation
FluxEs is a program for metabolic flux analysis using NMR spectra of tracer experiments.

FluxEs 1.0 is freely available via web interface. FluxEs 2.0 is a development version and will be made available via web interface upon request.

Non-profit organizations will, upon request, be granted a non-exclusive license to use the stand alone version of FluxEs 1.0 for internal research and teaching purposes at no charge.

FluxEs 2.0 (Windows) FluxEs 2.0 (Unix)
FluxEs 1.0 (Windows) FluxEs 1.0 (Unix)

MPI code for parallelized multiple alignment

Protein-protein interaction potential of mean force calculation scripts and datafiles
bioinformatics-2013-btt675.tgz Tar ball with python scripts, datafiles and TCR-pMHC (PDB ID:1AO7) use case.
Provides 'Availability and implementation' with May et al. (2013) Bioinformatics doi:10.1093/bioinformatics/btt675

16S rDNA-based analysis through mock data and simulations: data used in May et al. (2014)
Provides 454 data simulations (sff, fasta and read-taxonomy labels) used in May et al. (2014). Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.
README The README file detailing the folder structure and contents
CORE_1.tar.gz Tar gzipped archive for CORE_1 simulations
CORE_2.tar.gz Tar gzipped archive for CORE_2 simulations
M-pick patch HOWTO Instructions for applying the M-pick patch
M-pick patch M-pick patch file indicating changes made to M-pick

REPRO - Protein repeats analysis Program and exchange matrices: zipped archive; extract with: 'unzip'

SeRenDIP predicting protein interactions
SeRenDIP download page

TRUST repeat detection method
trust.tgz Program: tar gzipped archive; extract with: 'tar zxvf'

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