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    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.