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esl_compstruct - calculate accuracy of RNA secondary structure predictions

=head2 esl_construct

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

=head2 esl_histplot

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

=head2 esl_mask

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

=head2 esl_mixdchlet

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

=head2 esl_reformat

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

=head2 esl_selectn

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

=head2 esl_seqrange

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

=head2 esl_seqstat
  
    Alien::SeqAlignment::hmmer3->esl_seqstat (parameters & options);
esl_seqstat - summarize contents of a sequence file

=head2 esl_sfetch

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

=head2 esl_shuffle

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

=head2 esl_ssdraw

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

=head2 esl_translate

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

=head2 esl_weight

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

=head1 SEE ALSO

=over 4

=item * L<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. 


=item * L<Alien>

Documentation on the Alien concept itself.

=item * L<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. 

=item * L<Alien::Build::Manual::AlienUser|https://metacpan.org/dist/Alien-Build/view/lib/Alien/Build/Manual/AlienUser.pod>

Detailed manual for users of Alien classes.

=item * L<Bio::SeqAlignment|https://metacpan.org/pod/Bio::SeqAlignment>

A collection of tools and libraries for aligning biological sequences 
from within Perl. 

=back

=head1 AUTHOR

Christos Argyropoulos <chrisarg@gmail.com>

=head1 COPYRIGHT AND LICENSE