EnglishFrenchSpanish

OnWorks favicon

hhconsensus - Online in the Cloud

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

This is the command hhconsensus 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

PROGRAM:

NAME


hhconsensus - calculate the consensus sequence for an A3M/FASTA input file

SYNOPSIS


hhconsensus -i <file> [options]

DESCRIPTION


HHconsensus version 2.0.16 (January 2013) Calculate the consensus sequence for an
A3M/FASTA input file. (C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas
Hauser 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).

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

Output options:
-s <file>
append consensus sequence in FASTA (default=<infile.seq>)

-o <file>
write alignment with consensus sequence in A3M

-oa3m <file>
same

-oa2m <file>
write alignment with consensus sequence in A2M

-ofas <file>
write alignment with consensus sequence in FASTA

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

Filter input alignment (options can be combined):
-id [0,100] maximum pairwise sequence identity (%) (def=100)

-diff [0,inf[ filter most diverse set of sequences, keeping at least this

many sequences in each block of >50 columns (def=0)

-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)

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

Other options:
-addss add predicted secondary structure information from PSIPRED

Example: hhconsensus -i stdin -s stdout

Use hhconsensus online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    MSYS2
    MSYS2
    MSYS2 is a collection of tools and
    libraries providing you with an
    easy-to-use environment for building,
    installing and running native Windows
    software. It con...
    Download MSYS2
  • 2
    libjpeg-turbo
    libjpeg-turbo
    libjpeg-turbo is a JPEG image codec
    that uses SIMD instructions (MMX, SSE2,
    NEON, AltiVec) to accelerate baseline
    JPEG compression and decompression on
    x86, x8...
    Download libjpeg-turbo
  • 3
    Xtreme Download Manager
    Xtreme Download Manager
    The project has a new home now:
    https://xtremedownloadmanager.com/ For
    developers:
    https://github.com/subhra74/xdm Xtreme
    Download Manager is a powerful tool t...
    Download Xtreme Download Manager
  • 4
    TTGO VGA32 Lite
    TTGO VGA32 Lite
    Features:4:3 and 16:9 low resolution
    VGA outputPS/2 keyboard and mouse
    inputText-based user interface (TUI)
    with dialog managerPartial Unicode
    supportSlave dis...
    Download TTGO VGA32 Lite
  • 5
    Clover EFI bootloader
    Clover EFI bootloader
    Project has moved to
    https://github.com/CloverHackyColor/CloverBootloader..
    Features:Boot macOS, Windows, and Linux
    in UEFI or legacy mode on Mac or PC with
    UE...
    Download Clover EFI bootloader
  • 6
    unitedrpms
    unitedrpms
    Join us in Gitter!
    https://gitter.im/unitedrpms-people/Lobby
    Enable the URPMS repository in your
    system -
    https://github.com/UnitedRPMs/unitedrpms.github.io/bl...
    Download unitedrpms
  • More »

Linux commands

Ad