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