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hhconsensus - Online in the Cloud

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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

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