NAME

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

SYNOPSIS

       hhfilter -i infile -o outfile [options]

DESCRIPTION

       HHfilter 3.0.0 (15-03-2015) Filter an alignment by  maximum  pairwise  sequence  identity,
       minimum  coverage,  minimum  sequence  identity,  or  score per column to the first (seed)
       sequence.n(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