HHCONSENSUS(1)

💖 NAME 💖

hhconsensus — she calculates the consensus sequence for an A3M/FASTA input file. that's the whole job bestie, and she does it flawlessly. 💅

---

✨ SYNOPSIS ✨

hhconsensus -i <file> [options]

---

🦋 DESCRIPTION 🦋

okay so, HHconsensus 3.3.0 is the girl whose entire personality is: calculate the consensus sequence for an A3M/FASTA input file. iconic behavior, no notes. 🌸

(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

she's giving very much "I read the paper so you don't have to." 🫶

• -i <file> — the query alignment, which can be A2M, A3M, or FASTA. OR it can be a query HMM. either way she's ready. 💜

---

👑 Output options

• -s <file> — append the consensus sequence in FASTA (default=<infile.seq>). yes bestie, she'll just go ahead and pick a filename for you if you don't.
• -o <file> — write the alignment with the consensus sequence in A3M.
• -oa3m <file> — same. literally the same thing. twins. 🎀
• -oa2m <file> — write the alignment with the consensus sequence in A2M.
• -ofas <file> — write the alignment with the consensus sequence in FASTA.
• -v <int> — verbose mode, and the levels are: 0: no screen output, 1: only warings, 2: verbose. (yes, "warings" — that's literally how it's spelled in the source, we respect the lore 😭). so 1 is the chill one, 2 is her telling you everything.

---

🌈 Filter input alignment (options can be combined)

these ones stack, so go wild. 💅

• -id [0,100] — maximum pairwise sequence identity (%) (def=100).
• -diff [0,inf[ — filter the 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 the query (%) (def=0).
• -qid [0,100] — minimum sequence identity with the query (%) (def=0).
• -qsc [0,100] — minimum score per column with the query (def=-20.0). (yes the range says [0,100] and the default is -20.0. we don't ask questions, we just report. 🙈)

---

🧚 Input alignment format

• -M a2m — use A2M/A3M (this is the default!): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted).
• -M first — use FASTA: columns with a residue in the 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

look at her. reading from stdin, writing to stdout, zero drama, maximum slay. 🔥

---

hhconsensus 3.3.0+ds · August 2023 · this was hhconsensus(1) from User Commands, and yes she ate. 💖✨ bye bestie, go calculate a consensus sequence. 🦋