NAME
    Alien::SeqAlignment::edlib

VERSION
    version 0.02

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. 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. The build provides the static and shared
    libraries, but also the command line 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.

    <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.
    <https://metacpan.org/pod/Text::Levenshtein::XS> An XS library that
    computes edit distances but not alignment paths. This module was updated
    last in 2016 (see also its github repository at:
    https://github.com/ugexe/Text--Levenshtein--XS/)
    <https://metacpan.org/pod/Text::LevenshteinXS> Yet another XS
    implementation of Levenshtein distance over strings (no alignment path).
    This module was last updated in 2004.
    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.