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

# hhconsensus(1)

calculate the consensus sequence for an A3M/FASTA input file

## NAME

hhconsensus - calculate the consensus sequence for an A3M/FASTA input file

## SYNOPSIS

**hhconsensus** *-i \<file\>* \[*options*\]

## DESCRIPTION

HHconsensus 3.3.0 Calculate the consensus sequence for an A3M/FASTA input file. (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\>

  query alignment (A2M, A3M, or FASTA), or query HMM

### Output options:

- **-s** \<file\>

  append consensus sequence in FASTA (default=\<infile.seq\>)

- **-o** \<file\>

  write alignment with consensus sequence in A3M

- **-oa3m** \<file\>

  same

- **-oa2m** \<file\>

  write alignment with consensus sequence in A2M

- **-ofas** \<file\>

  write alignment with consensus sequence in FASTA

- **-v** \<int\>

  verbose mode: 0:no screen output  1:only warings  2: verbose

### Filter input alignment (options can be combined):

- **-id**

  \[0,100\] maximum pairwise sequence identity (%) (def=100)

**-diff** \[0,inf\[ filter most diverse set of sequences, keeping at least this

-

  many sequences in each block of \>50 columns (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)

### 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: hhconsensus **-i** stdin **-s** stdout