NAME
    Alien::SeqAlignment::edlib

VERSION
    version 0.05

SYNOPSIS
    To execute the alignment using the commande line tool:

     use Alien::Edlib;
     use Env qw( @PATH );

     unshift @PATH, Alien::SeqAlignment::edlib->bin_dir;
     system Alien::SeqAlignment::edlib->exe, (list of options), <queries.fasta>, <target.fasta>;

DESCRIPTION
    This distribution provides edlib so that it can be used by other Perl
    distributions that are on CPAN. The source code will be downloaded from
    the edlib 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 edlib 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 edlib library, and is guaranteed to use the latest
    version of edlib. The build provides the static and shared libraries,
    but also the CLI aligner (edlib-aligner, not currently available in
    Windows).

NAME
    Alien::SeqAlignment::edlib - find, build and install the edlib library

METHODS
  exe
     Alien::SeqAlignment::edlib->exe

    Returns the command name for running the CLI version of the edlib
    aligner Since the command line tool is not built under Windows by the
    edlib project make files, this method will return undef under Windows.

HELPERS
    %{edlib_aligner}

  edlib_aligner
    Returns the CLI command for the edlib aligner

SEE ALSO
    edlib <https://github.com/Martinsos/edlib>
        Edlib is a lightweight and superfast C/C++ library for sequence
        alignment using the edit (Levenshtein) distance between two or more
        biological (usually) sequences. It can calculate the edit distance,
        find the optimal aligment path and the coordinates (start/end)
        locations. It supports multiple alignment modes such as global (NW),
        prefix (SHW) and infix (HW). The library does not handle utf8 and
        its primary use is to compute edit distances and alignments over
        small (255 characters or fewer) alphabets as they occur in
        bioinformatic applications.

    Text::Levenshtein::Edlib
    <https://metacpan.org/pod/Text::Levenshtein::Edlib>
        An XS library that also wraps around the edlib library and returns
        edit distances, as well as alignment paths.

    Text::Levenshtein::XS <https://metacpan.org/pod/Text::Levenshtein::XS>
        An XS library that computes edit distances but not alignment paths.
        See also its github repository at:
        <https://github.com/ugexe/Text--Levenshtein--XS/>)

    Text::LevenshteinXS <https://metacpan.org/pod/Text::LevenshteinXS>
        Yet another XS implementation of Levenshtein distance over strings
        (no alignment path).

    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.

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.