Provided by: hhsuite_3.0~beta2+dfsg-3_amd64 
NAME
hhfilter - filter an alignment by maximum sequence identity of match states and minimum coverage
SYNOPSIS
hhfilter -i infile -o outfile [options]
DESCRIPTION
HHfilter 3.0.0 (15-03-2015) Filter an alignment by maximum pairwise sequence identity, minimum coverage,
minimum sequence identity, or score per column to the first (seed) sequence.n(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