(c) 2011-2012 The Authors, see LICENSE.txt for details.

[Dent Earl] (https://github.com/dentearl/)

The [Alignathon] (http://compbio.soe.ucsc.edu/alignathon/) is a collaborative project between whole genome aligners intended to help assess methods and promote development of the field. This repository is used to run analyses of predicted alignments within test packages.

• A Linux system to run the analysis pipeline
• Python 2.7
• [mafTools] (https://github.com/dentearl/maftools/)

1. Install dependencies.
2. $ git clone https://github.com/dentearl/mwgAlignAnalysis.git
3. $ cd mwgAlignAnalysis && make

After downloading a package from the [Alignathon website] (http://compbio.soe.ucsc.edu/alignathon/), performing an alignment and placing the predicted maf in package/predictions/, an analysis can be run using

$ make analysis location=/path/to/package set=testSet

where location is the path to the package and set is one of the prefixes from the registries directory, i.e. flySet, mammalSet, primateSet or testSet. The Makefile can be run in parallel with -j [integer] which allows the evaluations in an analysis to be run in parallel.