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# BMLSA

A Basic multi local sequence alignment tool using the Biopython implementation of the Smith-Waterman alignment algorithm.

## Features

 - Aligns a CSV of short sequences locally to a given reference sequence
 - Outputs in a CSV with old and new positions
 - Selectable parameters for alignment
 - Compatible with broad-range of input CSV formats
 - Automatically align with all sequences in reference FASTA
 - All produced output is human readable!

## More Information

For all live downloadable artifacts, build statuses, unit test results, and documentation, check out the continuous integration page for the [master branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/master/) ([development branch](https://ci.reslate.systems/job/ydeng/job/bmlsa/job/develop/)).