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