NAME

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

SYNOPSIS

       hhfilter -i infile -o outfile [options]

DESCRIPTION

       HHfilter 3.1.0  Filter  an  alignment  by  maximum  pairwise  sequence  identity,  minimum
       coverage, minimum sequence identity, or score per column to the first (seed) sequence.n(c)
       The HH-suite development team Steinegger M, Meier M, Mirdita M, V??hringer H,  Haunsberger
       S  J,  and  S??ding J (2019) HH-suite3 for fast remote homology detection and deep protein
       annotation.  bioRxiv, 560029. doi:10.1101/560029

       -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

   Other options:
       -maxseq <int>
              max number of input rows (def=65535)

       -maxres <int>
              max number of HMM columns (def=20001)

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