NAME

       csb-buildhmm - build an HMM from a FASTA sequence

DESCRIPTION

       usage: csb-buildhmm [-h] -q QUERY_ID [-t TK_ROOT] [-d DATABASE] [-c TK_CONFIG]

       [--cpu CPU] [--no-ss] [--no-pseudo] [--no-calibration]
              query

       Build an HMM from a FASTA sequence. This program is a proxy to hhblits/addss.pl and hhmake
       from the HHpred package. @note: assuming you have the full HHpred  package  installed  and
       configured.

   positional arguments:
       query  input sequence (FASTA or PDB file)

   optional arguments:
       -h, --help
              show this help message and exit

       -q QUERY_ID, --query-id QUERY_ID
              ID  of  the  query,  in PDB-like format (accessionCHAIN).Used for naming the output
              files.  Also, if the input is a PDB file with multiple chains,  CHAIN  is  used  to
              pull the required chain from the file.

       -t TK_ROOT, --tk-root TK_ROOT
              path     to     the     ToolkitRoot     folder     in     your     HHsuite    setup
              (default=/ebio/abt1_toolkit/share/wye)

       -d DATABASE, --database DATABASE
              custom HHblits database; if not defined, toolkit's unirpto20 will be used

       -c TK_CONFIG, --tk-config TK_CONFIG
              path to a folder containing custom HHsuite configs (e.g. HHPaths.pm) (default=.)

       --cpu CPU
              maximum degree of parallelism (default=1)

       --no-ss
              do not include secondary structure (default=False)

       --no-pseudo
              do not add emission and transition pseudocounts (default=False)

       --no-calibration
              do not calibrate the profile (default=False)

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.