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LICENSE  view on Meta::CPAN

TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.

                     END OF TERMS AND CONDITIONS

        Appendix: How to Apply These Terms to Your New Programs

  If you develop a new program, and you want it to be of the greatest
possible use to humanity, the best way to achieve this is to make it
free software which everyone can redistribute and change under these
terms.

  To do so, attach the following notices to the program.  It is safest to
attach them to the start of each source file to most effectively convey
the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.

    <one line to give the program's name and a brief idea of what it does.>
    Copyright (C) 19yy  <name of author>

README  view on Meta::CPAN

        parasail is a SIMD C (C99) library containing implementations of the
        Smith-Waterman (local), Needleman-Wunsch (global), and various
        semi-global pairwise sequence alignment algorithms. Here,
        semi-global means insertions before the start or after the end of
        either the query or target sequence are optionally not penalized.
        parasail implements most known algorithms for vectorized pairwise
        sequence alignment, including diagonal , blocked , striped , and
        prefix scan. Therefore, parasail is a reference implementation for
        these algorithms in addition to providing an implementation of the
        best-performing algorithm(s) to date on today's most advanced CPUs.

        parasail implements the above algorithms currently in three
        variants, 1) returning the alignment score and ending locations, 2)
        additionally returning alignment statistics (number of exact matches
        , number of similarities, and alignment length), and 3) functions
        that store a traceback for later retrieval as a SAM CIGAR string.
        The three variants exist because parasail is intended to be
        high-performing; calculating additional statistics or the traceback
        will perform slower than simply calculating the alignment score.

lib/Alien/SeqAlignment/parasail.pm  view on Meta::CPAN

=item * L<parasail|https://github.com/jeffdaily/parasail>

parasail is a SIMD C (C99) library containing implementations of the 
Smith-Waterman (local), Needleman-Wunsch (global), and various 
semi-global pairwise sequence alignment algorithms. Here, semi-global 
means insertions before the start or after the end of either the query 
or target sequence are optionally not penalized. parasail implements 
most known algorithms for vectorized pairwise sequence alignment, 
including diagonal , blocked , striped , and prefix scan. Therefore, 
parasail is a reference implementation for these algorithms in 
addition to providing an implementation of the best-performing 
algorithm(s) to date on today's most advanced CPUs.

parasail implements the above algorithms currently in three variants, 
1) returning the alignment score and ending locations, 
2) additionally returning alignment statistics (number of exact matches
, number of similarities, and alignment length), and 3) functions that 
store a traceback for later retrieval as a SAM CIGAR string. The three 
variants exist because parasail is intended to be high-performing; 
calculating additional statistics or the traceback will perform slower 
than simply calculating the alignment score.