---
name: "hhfilter"
section: "1"
platform: "linux"
package: "hhsuite"
version: "3.3.0+ds-8+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/hhfilter"
---

# hhfilter(1)

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

## 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