Metadata-Version: 2.1
Name: swalign
Version: 0.3.6
Summary: Smith-Waterman local aligner
Home-page: http://github.com/mbreese/swalign/
Author: Marcus Breese
Author-email: marcus@breese.com
License: UNKNOWN
Description: # swalign
        
        This package implements a Smith-Waterman style local alignment algorithm. You
        can align a query sequence to a reference. The scoring functions can be based
        on a matrix, or simple identity. Weights can be adjusted for match/mismatch
        and gaps, with gap extention penalties. Additionally, the gap penalty can be
        subject to a decay to prioritize long gaps.
        
        The input files are FASTA format sequences, or strings of sequences.
        
        Here is some skeleton code to get you started:
        
            import swalign
            # choose your own values here… 2 and -1 are common.
            match = 2
            mismatch = -1
            scoring = swalign.NucleotideScoringMatrix(match, mismatch)
        
            sw = swalign.LocalAlignment(scoring)  # you can also choose gap penalties, etc...
            alignment = sw.align('ACACACTA','AGCACACA')
            alignment.dump()
        
        For other uses, see the script in bin/swalign or https://compgen.io/projects/swalign
        
Platform: UNKNOWN
Requires-Python: >=3.1
Description-Content-Type: text/markdown
