NAME

       hhfilter - filter an alignment by maximum sequence identity of match states and minimum coverage

SYNOPSIS

       hhfilter -i infile -o outfile [options]

DESCRIPTION

       HHfilter  version  2.0.16 (January 2013) Filter an alignment by maximum sequence identity of match states
       and minimum coverage (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>
              read input file in A3M/A2M or FASTA format

       -o <file>
              write to output file in A3M format

       -a <file>
              append to output file in A3M format

OPTIONS

       -v <int>
              verbose mode: 0:no screen output  1:only warings  2: verbose

       -id    [0,100]  maximum pairwise sequence identity (%) (def=90)

       -diff [0,inf[
              filter MSA by selecting most diverse set of sequences, keeping at least this many seqs in each MSA
              block of length 50 (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)

       -neff [1,inf]
              target diversity of alignment (default=off)

   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

       Example: hhfilter -id 50 -i d1mvfd_.a2m -o d1mvfd_.fil.a2m