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

       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

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

-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)

   Inputalignmentformat:-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

   Otheroptions:-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)

hhfilter-iinfile-ooutfile [options]