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NAME

       HMMER - profile HMMs for biological sequence analysis

SYNOPSIS

       hmmalign
         Align sequences to a profile

       hmmbuild
         Construct profiles from multiple sequence alignments

       hmmconvert
         Convert profile file to various formats

       hmmemit
         Sample sequences from a profile

       hmmfetch
         Retrieve profiles from a file

       hmmlogo
         Produce a conservation logo graphic from a profile

       hmmpgmd
         Daemon for database search web services

       hmmpress
         Prepare a profile database for hmmscan

       hmmscan
         Search sequence(s) against a profile database

       hmmsearch
         Search profile(s) against a sequence database

       hmmsim
         Collect profile score distributions on random sequences

       hmmstat
         Summary statistics for a profile file

       jackhmmer
         Iteratively search sequence(s) against a sequence database

       makehmmerdb
         build nhmmer database from a sequence file

       nhmmer
         Search DNA/RNA queries against a DNA/RNA sequence database

       nhmmscan
         Search DNA/RNA sequence(s) against a DNA/RNA profile database

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

       alimask
         Calculate and add column mask to a multiple sequence alignment

DESCRIPTION

       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
       principle.

       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 (http://pfam.sanger.ac.uk).  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 (http://dfam.janelia.org).

       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.

SEE ALSO

       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
       package.

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

COPYRIGHT

       Copyright (C) 2018 Howard Hughes Medical Institute.
       Freely distributed under the BSD open source license.

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

AUTHOR

       http://eddylab.org