HHFILTER(1)							   User Commands						       HHFILTER(1)

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  2.0.15  (June  2012)	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

hhfilter 2.0.15 						     June 2012							       HHFILTER(1)