PyOpal 
¶
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
Overview¶
PyOpal is a Python module that provides bindings to Opal using Cython. It directly interacts with the trimAl internals, which has the following advantages:
no binary dependency: PyOpal is distributed as a Python package, so you can add it as a dependency to your project, and stop worrying about the Opal binary being present on the end-user machine.
no intermediate files: Everything happens in memory, in a Python object you control, so you don’t have to invoke the Opal CLI using a sub-process and temporary files.
better portability: Opal uses SIMD to accelerate alignment scoring, but doesn’t support dynamic dispatch, so it has to be compiled on the local machine to be able to use the full capabilities of the local CPU. PyOpal ships several versions of Opal instead, each compiled with different target features, and selects the best one for the local platform at runtime.
wider platform support: The Opal code has been backported to work on SSE2 rather than SSE4.1, allowing PyOpal to run on older x86 CPUs (all x86 CPUs support it since 2003). In addition, Armv7 and Aarch64 CPUs are also supported if they implement NEON extensions. Finally, the C++ code of Opal has been modified to compile on Windows.
Setup¶
Run pip install pyopal in a shell to download the latest release from PyPi,
or have a look at the Installation page to find other ways
to install pyopal.
Library¶
License¶
This library is provided under the MIT License. Opal was developed by Martin Šošić and is distributed under the terms of the MIT License as well.
This project is in no way not affiliated, sponsored, or otherwise endorsed by the original Opal authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.