# 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!