HHCONSENSUS

NAME

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

SYNOPSIS

hhconsensus -i <file> [options]

DESCRIPTION

HHconsensus 3.3.0 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. BMC Bioinformatics, doi:10.1186/s12859-019-3019-7
-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