Motif-Aware PRALINE (MA-PRALINE)

A motif-aware multiple sequence alignment tool. An article accompanying this software has been provisionally accepted for publication in PLOS Computational Biology; it can be found here.

Installing MA-PRALINE

Requirements

• Python 2.7 / Python 3.6 (earlier 3.x versions may also work, but have not been tested)
• An installation of PRALINE (https://github.com/ibivu/PRALINE)

Instructions

You can install MA-PRALINE by cloning this repository and running (in a shell):

python setup.py install

A version will be uploaded to PyPI in the near future, which should make MA-PRALINE installable with:

pip install mapraline

Extras

There is an additional repository at https://github.com/ibivu/MA-PRALINE-extras containing auxiliary code that was used to perform various analyses while developing MA-PRALINE. Although no support is provided for this code, some people may find it useful to, e.g. reparameterise MA-PRALINE or to calculate motif statistics.