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       HMMER - profile hidden Markov model software


              Align multiple sequences to a profile HMM.

              Build a profile HMM from a given multiple sequence alignment.

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

              Convert HMMER  profile  HMMs  to  other  formats,  such  as  GCG

              Generate sequences probabilistically from a profile HMM.

              Retrieve an HMM from an HMM database

              Create a binary SSI index for an HMM database

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

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


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


       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  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.


       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.


       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.

              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.

              Specifies the directory  location  of  HMM  databases.  Example: