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HHCONSENSUS(1) User Commands HHCONSENSUS(1)

NAME

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

SYNOPSIS

hhconsensus -i <file> [options]

DESCRIPTION

HHconsensus 3.1.0 Calculate the consensus sequence for an A3M/FASTA input file. (c) The HH-suite development team Steinegger M, Meier M, Mirdita M, V??hringer H, Haunsberger S J, and S??ding J (2019) HH-suite3 for fast remote homology detection and deep protein annotation. bioRxiv, 560029. doi:10.1101/560029
-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:

-maxseq <int>
max number of input rows (def=65535)

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

Example: hhconsensus -i stdin -s stdout

July 2019 hhconsensus 3.2.0