The HMMER software
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HMMER algorithms
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The following HMMER algorithms/programs are supported by this server:

phmmer
  used to search one or more query protein sequences against a protein sequence database

hmmscan
  search protein sequences against collections of profiles, such as Pfam. In HMMER2 this was called hmmpfam

hmmsearch
  used to search one or more profiles against a protein
  sequence database

jackhmmer
  iteratively search a query protein sequence, multiple
  sequence alignment or profile HMM against the target protein sequence
  database

This software has been released as part of the
HMMER software package (version 3.1)

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Other programs
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The following is a brief description of the other programs in the HMMER
suite. These are only available from downloaded distributions. However
they are used indirectly when performing the searches on the server

hmmalign
  performs a multiple sequence alignment of all the sequences
  (usually identified by running an hmmsearch) in the input, by aligning them individually to the profile HMM

hmmbuild
  builds a profile HMM for each multiple sequence alignment in
  the input multiple sequence alignment file, and saves it to a new file

hmmconvert
  utility converts an input profile file to different HMMER formats

hmmfetch
  retrieves one or more profile HMMs from a profile database

hmmpress
  takes a profile database in standard HMMER3 format and
  constructs binary compressed data files for hmmscan

hmmstat
  utility prints out a tabular file of summary statistics for each profile