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

VERSION
    version 0.02

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

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

    Now you can run the last tools as:

     system Alien::SeqAlignment::last->lastal (options);    
     system Alien::SeqAlignment::last->lastdb (options); 
     system Alien::SeqAlignment::last->maf_convert (options); 
     system Alien::SeqAlignment::last->train (options); 
     system Alien::SeqAlignment::last->split_or_splice (options); 
     system Alien::SeqAlignment::last->split_or_splice_pe (options); 
     system Alien::SeqAlignment::last->pe_probs (options);

DESCRIPTION
    This distribution provides last so that it can be used by other Perl
    distributions that are on CPAN. The source code will be downloaded from
    the last Gitlab repo, and if that fails it will use the location of a
    fork by the author of this Perl module. The build provides the various
    CLI tools in the last and last-pair-pe suites. Parallelization requires
    the installation of the GNU parallel package. If this is not available,
    the installation will terminate. In that case, install GNU Parallel from
    https://www.gnu.org/software/parallel/ and re-attempt installation of
    this Alien.

METHODS
  lastal
     Alien::SeqAlignment::last->lastal

    Returns the command name for running the CLI version of the last
    aligner. The latter finds local alignments between query sequences, and
    reference sequences that have been collected into a database using
    lastdb.

  dbbuild
     Alien::SeqAlignment::last->dbbuild

    Returns the command name for the application that builds the database of
    the reference sequences.

  maf_convert
     Alien::SeqAlignment::last->maf_convert

    Interconverts the MAF format with other multiple alignment formats. The
    formats currently supported are: axt, bed, blast, blasttab, chain, gff,
    html, psl, sam, tab. Note that per the author of last, the blast format
    is merely "blast-like", i.e. not identical to NCBI BLAST.

  last_train
     Alien::SeqAlignment::last->last_train

    last-train finds the rates (probabilities) of insertion, deletion, and
    substitutions between two sets of sequences. It thereby finds suitable
    substitution and gap scores for aligning them.

  split_or_splice
     Alien::SeqAlignment::last->split_or_splice

    This commnd provides access to last-split, which finds "split
    alignments" (typically for DNA) or "spliced alignments" (typically for
    RNA).

  split_or_splice_for_pe
     Alien::SeqAlignment::last->split_or_splice_for_pe

    This commnd provides access to last-split, which finds "split
    alignments" (typically for DNA) or "spliced alignments" (typically for
    RNA). It specifically targets paired-end reads. last-split-pe is a
    method that can split-align a short DNA read to a reference genome. It
    achieves high accuracy by combining probabilistic alignments with
    information from paired-end reads.

  pe_probs
     Alien::SeqAlignment::last->pe_probs

    This commnd provides access to last-pair-probs, which reads candidate
    alignments of paired DNA reads to a genome, and:

    * estimates the distribution of distances between paired reads, *
    estimates the probability that each alignment represents the genomic
    source of the read. These probabilities corresponds to a split alignment
    of the pair end read.

SEE ALSO
    *   LAST <https://gitlab.com/mcfrith/last/-/tree/main>

        LAST: find & align related regions of sequences LAST is designed for
        moderately large data (e.g. genomes, DNA reads, proteomes). It's
        especially good at:

        * Finding rearrangements and recombinations: the primary author
        claims that last-split does that more rigorously than anything else.
        * Finding DNA-versus-protein related regions, especially protein
        fossils. * Unusual data, e.g. AT-rich DNA, because we can fit
        parameters to the data and calculate significance. * Sensitive
        DNA-DNA search, due to fitting, sensitive seeding, and calculating
        significance.

        It can also: indicate the confidence/uncertainty of each column in
        an alignment, and use sequence quality data in a rigorous fashion.

    *   last-split-pe
        <https://bitbucket.org/splitpairedend/last-split-pe/wiki/Home>

        last-split-pe is a method that can split-align a short DNA read to a
        reference genome. It achieves high accuracy by combining
        probabilistic alignments with information from paired-end reads.

    *   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.

