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