NAME
    Alien::SeqAlignment::MMseqs2 - find, build and install the mmseqs2 tools

VERSION
    version 0.01

SYNOPSIS
    To execute the MMseqs2 set of tools, you can use the following code:

     use Alien::SeqAlignment::MMseqs2;
     use Env qw( @PATH );
     unshift @PATH, Alien::SeqAlignment::MMseqs2->bin_dir;

    Now you can run the mmseqs2 tools as:
    Alien::SeqAlignment::MMseqs2->mmseqs <command> [<args>]

DESCRIPTION
    This distribution provides MMseqs2 so that it can be used by other Perl
    distributions that are on CPAN. The source code will be downloaded from
    the MMseqs2 website, if it is not found in the system path. The program
    will then be built and installed in a private share location. The build
    provides the various CLI tools in the MMseqs2 suite.

METHODS : MMseqs2 SUITE
  mmseqs
      system Alien::SeqAlignment::MMseqs2->mmseqs <command> [<args>]

    Returns the command name for running the CLI version of the mmseqs2
    suite. The command is the name of the MMseqs workflow that you want to
    run.

SEE ALSO
    *   MMseqs2 <https://github.com/soedinglab/MMseqs2>

        MMseqs2: ultra fast and sensitive sequence search and clustering
        suite

        MMseqs2 (Many-against-Many sequence searching) is a software suite
        to search and cluster huge protein and nucleotide sequence sets.
        MMseqs2 is open source GPL-licensed software implemented in C++ for
        Linux, MacOS, and (as beta version, via cygwin) Windows. The
        software is designed to run on multiple cores and servers and
        exhibits very good scalability. MMseqs2 can run 10000 times faster
        than BLAST. At 100 times its speed it achieves a lmost the same
        sensitivity. It can perform profile searches with the same s
        ensitivity as PSI-BLAST at over 400 times its speed.

    *   Alien

        Documentation on the Alien concept itself.

    *   Alien::Base <https://metacpan.org/pod/Alien::Base>

        The base class for this Alien. The methods in that class allow you
        to use the static and the dynamic edlib library in your code.

    *   Alien::Build::Manual::AlienUser
        <https://metacpan.org/dist/Alien-Build/view/lib/Alien/Build/Manual/A
        lienUser.pod>

        Detailed manual for users of Alien classes.

    *   Bio::SeqAlignment <https://metacpan.org/pod/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) 2024 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.

