NAME

Alien::parasail

VERSION

version 1.232370

DESCRIPTION

This distribution provides parasail so that it can be used by other Perl distributions that are on CPAN. It does this by first trying to detect an existing install of parasail on your system. If found it 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

  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 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.

• Alien

  Documentation on the Alien concept itself.

• Alien::Base

  The base class for this Alien.

• Alien::Build::Manual::AlienUser

  Detailed manual for users of Alien classes.

AUTHOR

Christos Argyropoulos chrisarg@gmail.com

COPYRIGHT AND LICENSE

This software is copyright (c) 2023 by Christos Argyropoulos.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.