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