NAME

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

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