NAME

Alien::SeqAlignment::parasail - find, build and install the parasail library

VERSION

version 0.05

SYNOPSIS

To execute the alignment using the command line tool:

use Alien::parasail;
system Alien::SeqAlignment::parasail->parasail_aligner, (list of options);

DESCRIPTION

This distribution provides parasail so that it can be used by other Perl distributions that are on CPAN. The source code will be downloaded from the parasail github repo, and if that fails it will use the location of a fork but the author of this module. Contrary to other Alien modules, this one will not test for a prior install of the parasail library, but will install from source into a private share location for the use by other modules. This strategy will avoid overwritting prior system installs of the parasail library, and is guaranteed to use the latest version of parasail. The build provides the static and shared libraries, but also the CLI aligner (parasail_aligner).

METHODS

parasail_aligner

Alien::SeqAlignment::parasail->parasail_aligner

Returns the command name for running the CLI version of the parasail aligner.

SEE ALSO

• 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.

• 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.

• Bio::SeqAlignment

  A collection of tools and libraries for aligning biological sequences from within Perl.

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.