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      Alien::SeqAlignment::hmmer3->esl_compalign (parameters & options);
    esl_compalign - compare two multiple sequence alignments

  esl_compstruct
      Alien::SeqAlignment::hmmer3->esl_compstruct (parameters & options);
    esl_compstruct - calculate accuracy of RNA secondary structure predictions

  esl_construct
      Alien::SeqAlignment::hmmer3->esl_construct (parameters & options);
    esl_construct - describe or create a consensus secondary structure

  esl_histplot
      Alien::SeqAlignment::hmmer3->esl_histplot (parameters & options);
    esl_histplot - collate data histogram, output xmgrace datafile

  esl_mask
      Alien::SeqAlignment::hmmer3->esl_mask (parameters & options);
    esl_mask - mask sequence residues with Xs (or other characters)

  esl_mixdchlet
      Alien::SeqAlignment::hmmer3->esl_mixdchlet (parameters & options);
    esl_mixdchlet - fitting mixture Dirichlets to count data

  esl_reformat
      Alien::SeqAlignment::hmmer3->esl_reformat (parameters & options);
    esl_reformat - convert sequence file formats

  esl_selectn
      Alien::SeqAlignment::hmmer3->esl_selectn (parameters & options);
    esl_selectn - select random subset of lines from file

  esl_seqrange
      Alien::SeqAlignment::hmmer3->esl_seqrange (parameters & options);
    esl_seqrange - determine a range of sequences for one of many parallel

  esl_seqstat
        Alien::SeqAlignment::hmmer3->esl_seqstat (parameters & options);
    esl_seqstat - summarize contents of a sequence file

  esl_sfetch
      Alien::SeqAlignment::hmmer3->esl_sfetch (parameters & options);
    esl_sfetch - retrieve (sub-)sequences from a sequence file

  esl_shuffle
      Alien::SeqAlignment::hmmer3->esl_shuffle (parameters & options);
    esl_shuffle - shuffling sequences or generating random ones

  esl_ssdraw
      Alien::SeqAlignment::hmmer3->esl_ssdraw (parameters & options);
    esl_ssdraw - create postscript secondary structure diagrams

  esl_translate
      Alien::SeqAlignment::hmmer3->esl_translate (parameters & options);
    esl_translate - translate DNA sequence in six frames into individual

  esl_weight
      Alien::SeqAlignment::hmmer3->esl_weight (parameters & options);
    esl_weight - calculate sequence weights in MSA(s)

SEE ALSO
    *   HMMER <http://hmmer.org/>

        HMMER: biosequence analysis using profile hidden Markov models

        HMMER is used for searching sequence databases for sequence
        homologs, and for making sequence alignments. It implements methods
        using probabilistic models called profile hidden Markov models
        (profile HMMs).

        HMMER is often used together with a profile database, such as Pfam
        or many of the databases that participate in Interpro. But HMMER can
        also work with query sequences, not just profiles, just like BLAST.
        For example, you can search a protein query sequence against a
        database with phmmer, or do an iterative search with jackhmmer.

        HMMER is designed to detect remote homologs as sensitively as
        possible, relying on the strength of its underlying probability
        models. In the past, this strength came at significant computational
        expense, but as of the new HMMER3 project, HMMER is now essentially
        as fast as BLAST.

        HMMER can be downloaded and installed as a command line tool on your
        own hardware, and now it is also more widely accessible to the
        scientific community via new search servers at the European
        Bioinformatics Institute.

    *   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.