NAME

       HMMER - profile hidden Markov model software

SYNOPSIS

       hmm2align
              Align multiple sequences to a profile HMM.

       hmm2build
              Build a profile HMM from a given multiple sequence alignment.

       hmm2calibrate
              Determine  appropriate  statistical significance parameters for a profile HMM prior
              to doing database searches.

       hmm2convert
              Convert HMMER profile HMMs to other formats, such as GCG profiles.

       hmm2emit
              Generate sequences probabilistically from a profile HMM.

       hmm2fetch
              Retrieve an HMM from an HMM database

       hmm2index
              Create a binary SSI index for an HMM database

       hmm2pfam
              Search a profile HMM database with a sequence  (i.e.,  annotate  various  kinds  of
              domains in the query sequence).

       hmm2search
              Search  a sequence database with a profile HMM (i.e., find additional homologues of
              a modeled family).

DESCRIPTION

       These programs use profile hidden Markov  models  (profile  HMMs)  to  model  the  primary
       structure consensus of a family of protein or nucleic acid sequences.

OPTIONS

       All  HMMER  programs  give  a  brief  summary  of their command-line syntax and options if
       invoked without any arguments.  When invoked with the single argument, -h (i.e., help),  a
       program  will  report  more verbose command-line usage information, including rarely used,
       experimental, and expert options.  -h will report version numbers which are useful if  you
       need to report a bug or problem to me.

       Each  HMMER program has its own man page briefly summarizing command line usage.  There is
       also a user's guide that came with the software distribution, which  includes  a  tutorial
       introduction and more detailed descriptions of the programs.

       See http://hmmer.janelia.org/ for on-line documentation and the current HMMER release.

       In general, no command line options should be needed by beginning users.  The defaults are
       set up for optimum performance in most situations.   Options  that  are  single  lowercase
       letters  (e.g.  -a ) are "common" options that are expected to be frequently used and will
       be important in many applications.  Options that are single uppercase letters (e.g.  -B  )
       are  usually less common options, but also may be important in some applications.  Options
       that are full words (e.g.  --verbose ) are either rarely  used,  experimental,  or  expert
       options.   Some  experimental  options  are only there for my own ongoing experiments with
       HMMER, and may not be supported or documented adequately.

SEQUENCE FILE FORMATS

       In general, HMMER attempts to read most  common  biological  sequence  file  formats.   It
       autodetects  the format of the file. It also autodetects whether the sequences are protein
       or nucleic acid.  Standard IUPAC degeneracy codes are allowed in  addition  to  the  usual
       4-letter or 20-letter codes.

       Unaligned sequences
              Unaligned   sequence  files  may  be  in  FASTA,  Swissprot,  EMBL,  GenBank,  PIR,
              Intelligenetics, Strider, or GCG format.   These  formats  are  documented  in  the
              User's Guide.

       Sequence alignments
              Multiple  sequence  alignments  may be in CLUSTALW, SELEX, or GCG MSF format. These
              formats are documented in the User's Guide.

ENVIRONMENT VARIABLES

       For ease of using large stable sequence and HMM databases, HMMER looks for sequence  files
       and  HMM files in the current working directory as well as in system directories specified
       by environment variables.

       BLASTDB
              Specifies the directory location of sequence  databases.  Example:  /seqlibs/blast-
              db/.  In installations that use BLAST software, this environment variable is likely
              to already be set.

       HMMERDB
              Specifies the directory location of HMM databases. Example: /seqlibs/pfam/.