Alien-parasail

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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 [Wozniak, 1997], blocked [Rognes and
      Seeberg, 2000], striped [Farrar, 2007], and prefix scan [Daily,
      2015]. 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.
      Select the appropriate implementation for your needs.

README.md  view on Meta::CPAN

will use that.  If it cannot be found, the source code will be downloaded
from the internet and it will be installed in a private share location
for the use of other modules.

# SEE ALSO

- [parasail](https://github.com/jeffdaily/parasail)

    The parasail library home page.

    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 t...

    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), a...

- [Alien](https://metacpan.org/pod/Alien)

    Documentation on the Alien concept itself.

- [Alien::Base](https://metacpan.org/pod/Alien%3A%3ABase)

    The base class for this Alien.

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

for the use of other modules.

=head1 SEE ALSO

=over 4

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

The parasail library home page.

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 e...

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...

=item L<Alien>

Documentation on the Alien concept itself.

=item L<Alien::Base>

The base class for this Alien.