Scroll to navigation

HHFILTER(1) User Commands HHFILTER(1)


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


hhfilter -i infile -o outfile [options]


HHfilter 3.1.0 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. bioRxiv, 560029. doi:10.1101/560029
-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


-v <int>
verbose mode: 0:no screen output 1:only warings 2: verbose
[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)
[0,100] minimum coverage with query (%) (def=0)
[0,100] minimum sequence identity with query (%) (def=0)
[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

March 2020 hhfilter 3.2.0