.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.5.
.TH CSB-BUILDHMM "1" "November 2017" "csb-buildhmm 1.2.5" "User Commands"
.SH NAME
csb-buildhmm \- build an HMM from a FASTA sequence
.SH DESCRIPTION
usage: csb\-buildhmm [\-h] \fB\-q\fR QUERY_ID [\-t TK_ROOT] [\-d DATABASE] [\-c TK_CONFIG]
.TP
[\-\-cpu CPU] [\-\-no\-ss] [\-\-no\-pseudo] [\-\-no\-calibration]
query
.PP
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.
.SS "positional arguments:"
.TP
query
input sequence (FASTA or PDB file)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-q\fR QUERY_ID, \fB\-\-query\-id\fR 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.
.TP
\fB\-t\fR TK_ROOT, \fB\-\-tk\-root\fR TK_ROOT
path to the ToolkitRoot folder in your HHsuite setup
(default=/ebio/abt1_toolkit/share/wye)
.TP
\fB\-d\fR DATABASE, \fB\-\-database\fR DATABASE
custom HHblits database; if not defined, toolkit's
unirpto20 will be used
.TP
\fB\-c\fR TK_CONFIG, \fB\-\-tk\-config\fR TK_CONFIG
path to a folder containing custom HHsuite configs
(e.g. HHPaths.pm) (default=.)
.TP
\fB\-\-cpu\fR CPU
maximum degree of parallelism (default=1)
.TP
\fB\-\-no\-ss\fR
do not include secondary structure (default=False)
.TP
\fB\-\-no\-pseudo\fR
do not add emission and transition pseudocounts
(default=False)
.TP
\fB\-\-no\-calibration\fR
do not calibrate the profile (default=False)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.