hhconsensus(1) 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