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    hmmsearch - search profile against sequence database

  hmmpress
      Alien::SeqAlignment::hmmer3->hmmpress (parameters & options);
    hmmpress - prepare profile database for hmmscan

  phmmer
      Alien::SeqAlignment::hmmer3->phmmer (parameters & options);
    phmmer - search single sequence against sequence database

  jackhmmer
      Alien::SeqAlignment::hmmer3->jackhmmer (parameters & options);
    jackhmmer - iteratively search single sequence against database

  nhmmer
      Alien::SeqAlignment::hmmer3->nhmmer (parameters & options);
    nhmmer - search DNA query against DNA sequence database

  nhmmscan
      Alien::SeqAlignment::hmmer3->nhmmscan (parameters & options);
    nhmmscan - search DNA sequence against a DNA profile database

  hmmstat
      Alien::SeqAlignment::hmmer3->hmmstat (parameters & options);
    hmmstat - show summary statistics for a profile file

  makehmmerdb
      Alien::SeqAlignment::hmmer3->makehmmerdb (parameters & options);
    makehmmerdb - prepare an nhmmer binary database

  hmmsim
      Alien::SeqAlignment::hmmer3->hmmsim (parameters & options);
    hmmsim - collect score distributions on random sequences

METHODS : EASEL SUITE
    Note that the names of the methods are the same as the functions in the
    CLI of the EASEL suite, but with the "-" replaced by "_", e.g.
    esl-afetch becomes esl_afetch.

  esl_afetch
      Alien::SeqAlignment::hmmer3->esl_afetch (parameters & options);
    esl_afetch - retrieve alignments from a multi-MSA database

  esl_alimanip
      Alien::SeqAlignment::hmmer3->esl_alimanip (parameters & options);
    esl_alimanip - manipulate a multiple sequence alignment

  esl_alimap
      Alien::SeqAlignment::hmmer3->esl_alimap (parameters & options);
    esl_alimap - map two alignments to each other

  esl_alimask
      Alien::SeqAlignment::hmmer3->esl_alimask (parameters & options);

  esl_alimerge
        Alien::SeqAlignment::hmmer3->esl_alimerge (parameters & options);
    esl_alimerge - merge alignments based on their reference (RF) annotation

  esl_alipid
      Alien::SeqAlignment::hmmer3->esl_alipid (parameters & options);
    esl_alipid - calculate pairwise percent identities for all sequence

  esl_alirev
      Alien::SeqAlignment::hmmer3->esl_alirev (parameters & options);
    esl_alirev - reverse complement a multiple alignment

  esl_alistat
      Alien::SeqAlignment::hmmer3->esl_alistat (parameters & options);
    esl_alistat - summarize a multiple sequence alignment file

  esl_compalign
      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