MIGA documentation¶
Introduction¶
MIGA is a Python package that provides a MSA (Multiple Sequence Alignment) mutual information genetic algorithm optimizer. It sorts two MSAs in a way that maximize or minimize their mutual information. The genetic algorithm solvers may run on both CPU and Nvidia GPUs.
This code is available under the GNU Lesser General Public License, version 3 (see LICENSE file).
Requirements¶
- Python version 3+
- GCC and G++
- Numpy
Optional requirements¶
- CUDA capable GPU with compute capability >= 3.0
- CUDA Toolkit version 9+
- Cython 0.22+
Instalation¶
CUDA builds¶
For CUDA enabled installation, make sure the CUDA_HOME
is set and pointing to a valid CUDA 9+ installation root.
Pip¶
Run pip install miga
From source¶
- Make sure Cython version 0.22+ is installed
- Clone this repository
- Run
git submodule update --init --recursive
to update submodules - Optionally set the environment variable
CUDA_HOME
to point to your CUDA Toolkit installation - Run
pip install miga/package
Usage¶
Plese refer to the examples folder and to online documentation to learn how to use this package.
Bugs and feature requests¶
Please report bugs and feature requests through the Issues page.