data wrangling for
computational genomics
 

swalign

swalign is a version of a standard Smith-Waterman local alignment algorithm written in Python. It is a useful example of how one might write an aligner from scratch. It is not a highly performant example, but it is a useful teaching tool or for quick and dirty alignment searches when building an index would be overkill.

The aligner can be used in a stand-alone mode or as an importable Python library.