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       HMMER - profile HMMs for biological sequence analysis


         Align sequences to a profile

         Construct profile(s) from multiple sequence alignment(s)

         Convert profile file to various HMMER and non-HMMER formats

         Sample sequences from a profile

         Retrieve profile HMM(s) from a file

         Daemon used for web server, for phmmer-, hmmsearch-, and hmmscan-like search

         Prepare an HMM database for hmmscan

         Search protein sequence(s) against a protein profile database

         Search protein profile(s) against a protein sequence database

         Collect profile score distributions on random sequences

         Summary statistics for a profile file

         Iterative search of a protein sequence against a protein sequence database

         Search nucleotide sequence(s), alignment(s), or profile(s) against a nucleotide sequence

         Search nucleotide sequence(s) against a nucleotide profile database

         Search a protein sequence(s) against a protein sequence database


       HMMER is a suite of several  programs  for  biological  sequence  alignment  and  database
       homology  search.  It  uses  probabilistic  models  called  "profile hidden Markov models"
       (profile HMMs) to represent the likely evolutionary homologs of a  single  sequence  or  a
       multiple  alignment  of  a  sequence  family.  A main avenue of research is to improve the
       evolutionary predictive models in HMMER to be  able  to  recognize  and  accurately  align
       increasingly remote homologs, distant in time.

       HMMER is also used as an organizational tool, to group the exponentially growing number of
       biological sequences into a vastly smaller set of well-annotated  sequence  families.  New
       sequences  can  be  annotated  by  comparison against curated sequence family databases of
       prebuilt HMMER profiles, in addition or instead  of  comparison  to  the  entire  sequence
       database.  Databases  such  as  Pfam, SMART, and TIGRfams, among others, are based on this

       HMMER is used in three main modes: to search a sequence database for  new  homologs  of  a
       sequence or a sequence family; to search a profile database (like Pfam) to find what known
       family a query sequence belongs to, or what domains it has; and to automatically construct
       large multiple alignments (i.e. with an effectively unlimited number of sequences) using a
       profile representative of a sequence family.

       Suppose you have a multiple sequence alignment of a sequence family of interest,  and  you
       want  to  search  a sequence database for additional homologs. The hmmbuild program builds
       profile(s) from multiple alignment(s).  The hmmsearch program searches protein  profile(s)
       against  a  protein sequence database, and nhmmer searches nucleotide profile(s) against a
       nucleotide sequence database.

       Suppose you have a single sequence of interest, and you want to search a sequence database
       for  additional  homologs. The phmmer program searches a single protein sequence against a
       protein sequence database. The jackhmmer program does the same thing  but  iteratively  --
       homologs  detected  in  a  previous round are incorporated into a new profile, and the new
       profile is searched again.  phmmer is used like BLASTP,  and  jackhmmer  is  used  like  a
       protein  PSI-BLAST.  The  nhmmer  program  searches a single nucleotide sequence against a
       nucleotide sequence.

       Suppose you have sequence(s) that you want to analyze  using  a  HMMER-based  profile  HMM
       database like Pfam (  The hmmpress program formats a profile HMM
       flatfile (such as the file you would download from Pfam) into  a  HMMER  binary  database.
       The  hmmscan  program  searches  protein  sequence(s) against that database.  The nhmmscan
       program can  similarly  search  nucleotide  sequence(s)  against  a  pressed  database  of
       nucleotide profiles, such as from Dfam (

       Suppose  you  want  to  align  lots  of  sequences.  You  can construct a manageably small
       alignment of a representative set of sequences, build a profile with hmmbuild, and use the
       hmmalign program to align any number of sequences to that profile.

       HMMER  also  includes  some  auxiliary  tools  for  working  with large profile databases.
       hmmfetch fetches one or more profiles from a database.  hmmstat prints summary  statistics
       about a profile file.

       For  compatibility  with  other  profile  software  and  previous  versions  of HMMER, the
       hmmconvert program converts profiles to a few other formats. We intend to add more support
       for other formats over time.

       The  hmmemit  program  generates  (simulates)  "homologous"  sequences  by sampling from a
       profile. It can also generate a "consensus" sequence.

       The hmmsim program is a simulator used for collecting statistics about score distributions
       on random sequences.

       Each program has its own man page.


       This  is  a  summary  man  page  for  the entire HMMER3 package.  See individual man pages
       [hmmbuild(1), for example] for usage, options, and description  of  each  program  in  the

       For  complete  documentation,  see  the  user guide that came with your HMMER distribution
       (Userguide.pdf); or see the HMMER web page ().


       Copyright (C) 2015 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

       For additional information on copyright and licensing, see the file  called  COPYRIGHT  in
       your HMMER source distribution, or see the HMMER web page ().


       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA