Maligner is a tool for aligning molecular or insilico restriction maps to a reference map. Maligner comes with several different modes of alignment:

• maligner_dp: Uses dynamic program and allows global-local alignments of a query against a reference. Allows for unmatched sites in both the query and reference.

• malign_ix : Uses a more restrictive but faster mode of index based alignment.

• malign_vd : Allows for partial prefix or suffix alignments of a query against a reference, which can be used to find split alignments.

Maligner is built using cmake, which can be installed using your package manager. Building Maligner requires a C++ compiler C++11 support.

To build with cmake,

git clone https://github.com/LeeMendelowitz/maligner.git maligner
cd maligner # Make sure you are in the repo directory
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
make install

This will install compiled binaries maligner_dp, maligner_ix, and maligner_vd and additional python utility scripts into the directory build/bin.

The malignpy python package is installed to build/lib. Many of the Maligner utility scripts for working with maps files and alignment files depend on malignpy. In order to use these scripts, you must symlink malignpy into your working directory or modify your PYTHONPATH environment variable:

export PYTHONPATH=/path/to/build/lib:$PYTHONPATH

Building Maligner requires a C++ compiler with C++11 support. The build has been tested with g++ 4.8.3 on Red Hat Linux and Apple LLVM 6.0 on Mac OS X.

Maligner also comes with several python scripts for working with and converting alignment files. These scripts require the following python libraries: numpy, scipy, pandas, and BioPython.

You can install these dependencies using pip:

pip install -r requirements.txt

• See the ecoli example script in the repository.

• See the wiki

• Ask for command line help: maligner_dp --help