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

Distributed packages

  1. Download the latest release.
  2. Run pip install miga.version.tar.gz

From source

  1. Make sure Cython version 0.22+ is installed
  2. Clone this repository
  3. Run git submodule update --init --recursive to update submodules
  4. Optionally set the environment variable CUDA_HOME to point to your CUDA Toolkit installation
  5. 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.

Benchmark

Contents:

Indices and tables