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).
- -i <file>
- query alignment (A2M, A3M, or FASTA), or query HMM
- -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
- -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)
- -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
-maxres <int> max number of HMM columns
(def=20001)
Example: hhconsensus -i stdin -s stdout