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csb-buildhmm - build an HMM from a FASTA sequence


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

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

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

positional arguments:

input sequence (FASTA or PDB file)

optional arguments:

show this help message and exit
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.
path to the ToolkitRoot folder in your HHsuite setup (default=/ebio/abt1_toolkit/share/wye)
custom HHblits database; if not defined, toolkit's unirpto20 will be used
path to a folder containing custom HHsuite configs (e.g. (default=.)
maximum degree of parallelism (default=1)
do not include secondary structure (default=False)
do not add emission and transition pseudocounts (default=False)
do not calibrate the profile (default=False)


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

November 2017 csb-buildhmm 1.2.5