This is a fast implementation of the Landau-Vishkin-Nussinov algorithm for pair-wise alignment of sequences.

This library uses CMAKE to build libraries (static and shared) and binaries (apps and tests). Execute following commands to build it using CMAKE:

1. cd build
2. cmake -D CMAKE_BUILD_TYPE=Release ..
3. make

This will create binaries in build/bin/ directory and libraries (static and shared) in build/lib/ directory. You can run ./test.sh to confirm that the installation was successful.

Also there is a simple build script provided in the repository, which is executed by running ./build.sh from the root directory.

This implementation is available as a standalone library, but it also offers a simple executable named main that can be found in the build/bin/ directory. This executable is run from the command line, where the first argument should be SHW for prefix alignment, NW for global, and HW for infix alignment. The second and third arguments represent the path to the files containing FASTA representations of the pattern and text for which the alignment should be calculated. Next argument denotes the number of repetitions, and the final argument represents a boolean value which tells the program whether or not it should also reconstruct the alignment path. This is returned in the CIGAR format.

Detailed explanation of this implementation is available in the Paper directory of this repository, but unfortunately the paper is only available in Croatian.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC339353/pdf/nar00270-0052.pdf

https://github.com/Martinsos/edlib