CCMgen and CCMpredPy

CCMgen is a Python toolkit for sampling protein-like sequences from a second-order Markov Randon Field model. By using second-order interactions, sampled protein sequences are more realistic than what can be sampled from e.g. a model using only a PSSM representation.

CCMgen is accompanied by CCMpredPy, a fast Python implementation of an evolutionary coupling method for learning a Markov Randon Field Model from the multiple sequence alignment of a protein family by either state-of-the-art pseudo-likelihood maximization (less accurate) or persistent contrastive divergence (recommended for use with CCMgen). The coupling potentials encoded by the learned Markov Random Field model can be used with CCMgen to generate new sequences.

License

CCMgen and CCMpredPy are released under the GNU Affero GPL License, version 3.0 or later.

Requirements

CCMgen/CCMpredPy was developed and tested with Python 3.6 and requires the following Python packages installed on your system:

• NumPy (pip install numpy)
• SciPy (pip install scipy)
• BioPython (pip install biopython)
• MsgPack (pip install msgpack-python)
• six (pip install six)
• plotly (pip install plotly)
• colorlover (pip install colorlover)

or, in one command:

pip install numpy scipy biopython msgpack-python six plotly colorlover

Download

Release Versions

Please check out the [GitHub releases page for CCMgen](TODO TODO TODO) to download a stable CCMgen/CCMpredPy release. After you're done downloading and extracting, please follow the installation instructions below.

Development Versions from Git

To clone CCMgen/CCMpredPy directly from git, please use the following command line:

git clone https://github.com/soedinglab/ccmgen.git

Installation

There are some C libraries to speed up crucial parts of the calculations that need to be compiled. Change to the main directory and from there for a system-wide installation run:

<!--- ```bash python setup.py build_ext --inplace ``` -->

pip install .

or for a local installation run (creates symlink to the repository in your environment):

pip install -e .

Alternatively, you can install the latest development version of CCMgen/CCMpredPy with pip directly from this repository without the need of cloning by running:

pip install git+https://github.com/susannvorberg/CCmpredPy@master

and keep updated by running:

pip install git+https://github.com/susannvorberg/CCmpredPy@master --upgrade

Note: When installing on osx, make sure to use an appropriate gcc compiler and not clang, e.g. by setting export CC=/usr/local/Cellar/gcc/X.X.X/bin/gcc-X if gcc was installed via brew.

Next Steps

Now you're ready to use CCMgen and CCMpredPy! You can have a look at the getting started guide to learn how to use both tools.