DOKK / manpages / debian 10 / hhsuite / hhconsensus.1.en
HHCONSENSUS(1) User Commands HHCONSENSUS(1)

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

hhconsensus -i <file> [options]

HHconsensus 3.0.0 (15-03-2015) 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).

query alignment (A2M, A3M, or FASTA), or query HMM

append consensus sequence in FASTA (default=<infile.seq>)
write alignment with consensus sequence in A3M
same
write alignment with consensus sequence in A2M
write alignment with consensus sequence in FASTA
verbose mode: 0:no screen output 1:only warings 2: verbose

[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)
[0,100] minimum coverage with query (%) (def=0)
[0,100] minimum sequence identity with query (%) (def=0)
[0,100] minimum score per column with query (def=-20.0)

use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted)
use FASTA: columns with residue in 1st sequence are match states
use FASTA: columns with fewer than X% gaps are match states

-maxres <int> max number of HMM columns (def=20001)

Example: hhconsensus -i stdin -s stdout

February 2019 hhconsensus 3.0~beta3+dfsg