OnWorks favicon

hhmake - Online in the Cloud

Run hhmake in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command hhmake that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



hhmake - build an HMM from an input alignment or convert between HMMER format and HHsearch


hhmake -i file [options]


HHmake version 2.0.16 (January 2013) Build an HMM from an input alignment in A2M, A3M, or
FASTA format, or convert between HMMER format (.hmm) and HHsearch format (.hhm). Remmert
M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast iterative protein sequence
searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011). (C) Johannes Soeding,
Michael Remmert, Andreas Biegert, Andreas Hauser

-i <file>
query alignment (A2M, A3M, or FASTA), or query HMM

Output options:
-o <file>
HMM file to be written to (default=<infile.hhm>)

-a <file>
HMM file to be appended to

-v <int>
verbose mode: 0:no screen output 1:only warings 2: verbose

-seq <int>
max. number of query/template sequences displayed (def=10) Beware of overflows! All
these sequences are stored in memory.

-cons make consensus sequence master sequence of query MSA

-name <name>
use this name for HMM (default: use name of first sequence)

Filter query multiple sequence alignment

-id [0,100] maximum pairwise sequence identity (%) (def=90)

-diff [0,inf[
filter MSA by selecting most diverse set of sequences, keeping at least this many
seqs in each MSA block of length 50 (def=100)

-cov [0,100] minimum coverage with query (%) (def=0)

-qid [0,100] minimum sequence identity with query (%) (def=0)

-qsc [0,100] minimum score per column with query (def=-20.0)

-neff [1,inf]
target diversity of alignment (default=off)

Input alignment format:
-M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' =
gaps aligned to inserts (may be omitted)

-M first
use FASTA: columns with residue in 1st sequence are match states

-M [0,100]
use FASTA: columns with fewer than X% gaps are match states

Pseudocount (pc) options:
-pcm 0-2 position dependence of pc admixture 'tau' (pc mode, default=0)

0: no pseudo counts:
tau = 0

1: constant
tau = a

2: diversity-dependent: tau = a/(1 + ((Neff[i]-1)/b)^c) (Neff[i]: number of
effective seqs in local MSA around column i) 3: constant diversity pseudocounts

-pca [0,1] overall pseudocount admixture (def=1.0)

-pcb [1,inf[ Neff threshold value for -pcm 2 (def=1.5)

-pcc [0,3] extinction exponent c for -pcm 2 (def=1.0)

-pre_pca [0,1]
PREFILTER pseudocount admixture (def=0.8)

-pre_pcb [1,inf[ PREFILTER threshold for Neff (def=1.8)

Context-specific pseudo-counts:
use substitution-matrix instead of context-specific pseudocounts

-contxt <file> context file for computing context-specific pseudocounts

<file> column state file for fast database prefiltering (default=./data/cs219.lib)

Example: hhmake -i test.a3m

Use hhmake online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    LMMS Digital Audio Workstation
    LMMS Digital Audio Workstation
    LMMS is a free cross-platform software
    which allows you to produce music with
    your computer. If you like this project
    consider getting involved in the project
    Download LMMS Digital Audio Workstation
  • 2
    FreeRTOS Real Time Kernel (RTOS)
    FreeRTOS Real Time Kernel (RTOS)
    FreeRTOS is a market-leading real-time
    operating system (RTOS) for
    microcontrollers and small
    microprocessors. Distributed freely
    under the MIT open source lice...
    Download FreeRTOS Real Time Kernel (RTOS)
  • 3
    Avogadro is an advanced molecular
    editor designed for cross-platform use
    in computational chemistry, molecular
    modeling, bioinformatics, materials
    science and ...
    Download Avogadro
  • 4
    XMLTV is a set of programs to process
    TV (tvguide) listings and help manage
    your TV viewing, storing listings in an
    XML-based format. There are utilities to
    Download XMLTV
  • 5
    Strikr Free Software project. Artifacts
    released under a 'intent based'
    dual license: AGPLv3 (community) and
    CC-BY-NC-ND 4.0 international
    Download strikr
  • 7
    giflib is a library for reading and
    writing gif images. It is API and ABI
    compatible with libungif which was in
    wide use while the LZW compression
    algorithm was...
    Download GIFLIB
  • More »

Linux commands