CCMgen
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soedinglab
Hello, When running the [simple example provided in your wiki](https://github.com/soedinglab/ccmgen/wiki/Compute-and-Visualize-Contact-Maps), CCMpred failed with the following error in ccmpred/algorithm/lbfgs.py, line 91, in minimize: `AttributeError: 'str' object has no attribute 'decode'` It...
Hi, I would like to infer a model on a generated data set where "proteins" have only 2 states available for each site. For example : ``` MSA = [...
the ccmpred.parameter_handling.structured_to_linear() function linearizes x_single and x_pair. by default it is assumed that x_single is a vector of size (L,20), if the flag nogapstate=False, it's assumed x_single is (L,21). So...
Dear all, I noticed that the "matrianglify" function did not yield the correct output for the BLOSUM62 matrix given in the same file. It was a problem of indexes, so...
Hello, Since pseudo-likelihood is optimized on the MSA and not on the frequencies, pseudo-counts are not actually used (except for v* centering). Do you plan on working on this in...
https://github.com/soedinglab/CCMgen/blob/d874668e176a8821ac8c5794a8805f1b6eb9b397/ccmpred/sampling/__init__.py#L37 The current implementation uses the rounded expectation over the full sequence as the number of mutations `nmut` . This can be problematic in edge cases (sequences very short or...
