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lib/Alien/SeqAlignment/hmmer3.pm  view on Meta::CPAN

jackhmmer - iteratively search single sequence against database

=head2 nhmmer

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

=head2 nhmmscan

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

=head2 hmmstat

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

=head2 makehmmerdb

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

=head2 hmmsim

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

=head1 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.

=head2 esl_afetch

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

=head2 esl_alimanip

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

=head2 esl_alimap

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

=head2 esl_alimask

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

=head2 esl_alimerge
  
    Alien::SeqAlignment::hmmer3->esl_alimerge (parameters & options);
esl_alimerge - merge alignments based on their reference (RF) annotation

=head2 esl_alipid

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

=head2 esl_alirev

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

=head2 esl_alistat

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

=head2 esl_compalign

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

=head2 esl_compstruct

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