NAME

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

SYNOPSIS

       hhfilter -i infile -o outfile [options]

DESCRIPTION

       HHfilter  3.3.0  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.  BMC Bioinformatics, doi:10.1186/s12859-019-3019-7

       -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

hhfilter 3.3.0+ds                                  August 2023                                       HHFILTER(1)