---
name: "csb-buildhmm"
section: "1"
platform: "linux"
package: "csb"
version: "1.2.5+dfsg-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/csb-buildhmm"
---

# csb-buildhmm(1)

build an HMM from a FASTA sequence

## 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.