matlab

matlab scripts or modules

GaussDCA: Multivariate Gaussian Inference of Protein Contacts from Multiple Sequence Alignment

AttachmentSize
GaussDCA-julia.tgz25.09 KB
GaussDCA-matlab.tgz24.36 KB

This is the code which accompanies the paper "Fast and accurate multivariate Gaussian modeling of protein families: Predicting residue contacts and protein-interaction partners" by Carlo Baldassi, Marco Zamparo, Christoph Feinauer, Andrea Procaccini, Riccardo Zecchina, Martin Weigt and Andrea Pagnani, (2014) PLoS ONE 9(3): e92721. doi:10.1371/journal.pone.0092721

The code comes in two versions, one for Julia and one for MATLAB. They provide nearly identical funcitionality. The Julia code is slightly faster, and doesn't require compilation of external modules.

Julia code

You can download the Julia code from the attached file "GaussDCA-julia.tgz"; however, the recommended way to obtain the code is by using the command Pkg.clone("https://github.com/carlobaldassi/GaussDCA.jl") in the julia command line. See also the documentation at https://github.com/carlobaldassi/GaussDCA.jl.

Matlab code

You can download the MATLAB code from the attached file "GaussDCA-matlab.tgz", or from https://github.com/carlobaldassi/GaussDCA.matlab. See the README.md file for instructions.

Prize-Collecting Steiner Trees

AttachmentSize
msgsteiner.tgz6.84 KB
msgsteiner-1.1.tgz10.35 KB

This is the distribution package of MSGSTEINER

The permission to use this software is granted by the authors, Alfredo
Braunstein and Riccardo Zecchina, only on the following 5 conditions:

BP for the diluted perceptron

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dilperc.tgz14.1 KB

This is code for biological data analysis using a multi-state diluted discrete perceptron.
It contains also a matlab mex implementation.

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