HHMAKE(1)

okay bestie, you just opened HHMAKE(1) 🫶 that's the manual page for hhmake, and ngl it's lowkey doing the most: it builds an HMM and it converts between HMMER format and HHsearch format. two jobs, zero complaints, main character energy fr fr 👑

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🌸 NAME 🌸

hhmake — build an HMM from an input alignment, or convert between HMMER format and HHsearch format 💅

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📜 SYNOPSIS 📜

hhmake -i <file> -o <file> [options]

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✨ DESCRIPTION ✨

HHmake 3.3.0, bestie. Build an HMM from an input alignment in A2M, A3M, or FASTA format, or convert between HMMER format (.hmm) and HHsearch format (.hhm). that's it, that's the girl 💖

the receipts, because we always cite our sources 🎀

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 (c) The HH-suite development team

• -i <file> — your query alignment (A2M, A3M, or FASTA), or a query HMM 🧬

quick heads up: <file> may be 'stdin' or 'stdout' throughout. all of it. every time. iconic behavior honestly.

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💾 Output options 💾

• -o <file> — the HMM file to be written to (default=<infile.hhm>) ✍️
• -a <file> — HMM file to be appended to
• -v <int> — verbose mode: 0:no screen output, 1:only warings, 2: verbose
• -seq <int> — max. number of query/template sequences displayed (def=10). Beware of overflows! All these sequences are stored in memory 😭
• -add_cons — make consensus sequence master sequence of query MSA 👑
• -name <name> — use this name for HMM (default: use name of first sequence)

🧹 Filter query multiple sequence alignment 🧹

• -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=100)
• -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

🍓 Pseudocount (pc) options 🍓

Context specific hhm pseudocounts:

• -pc_hhm_contxt_mode {0,..,3} — position dependence of pc admixture 'tau' (pc mode, default=0)
  • 0: no pseudo counts — tau = 0
  • 1: constant — tau = a
  • 2: diversity-dependent — tau = a/(1+((Neff[i]-1)/b)^c)
  • 3: CSBlast admixture — tau = a(1+b)/(Neff[i]+b) (Neff[i]: number of effective seqs in local MSA around column i)
• -pc_hhm_contxt_a [0,1] — overall pseudocount admixture (def=0.9)
• -pc_hhm_contxt_b [1,inf[ — Neff threshold value for mode 2 (def=4.0)
• -pc_hhm_contxt_c [0,3] — extinction exponent c for mode 2 (def=1.0)

Context independent hhm pseudocounts (used for templates; used for query if contxt file is not available):

• -pc_hhm_nocontxt_mode {0,..,3} — position dependence of pc admixture 'tau' (pc mode, default=2)
  • 0: no pseudo counts — tau = 0
  • 1: constant — tau = a
  • 2: diversity-dependent — tau = a/(1+((Neff[i]-1)/b)^c) (Neff[i]: number of effective seqs in local MSA around column i)
• -pc_hhm_nocontxt_a [0,1] — overall pseudocount admixture (def=1.0)
• -pc_hhm_nocontxt_b [1,inf[ — Neff threshold value for mode 2 (def=1.5)
• -pc_hhm_nocontxt_c [0,3] — extinction exponent c for mode 2 (def=1.0)

Context-specific pseudo-counts:

• -nocontxt — use substitution-matrix instead of context-specific pseudocounts
• -contxt <file> — context file for computing context-specific pseudocounts (default=)

🌈 Other options 🌈

• -maxseq <int> — max number of input rows (def=65535)
• -maxres <int> — max number of HMM columns (def=20001)

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🌟 Example 🌟

hhmake -i test.a3m -o stdout

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and that's the whole page, bestie 🫶 this one came from hhmake 3.3.0+ds, dated August 2023, and it lives at home as HHMAKE(1) 💖 go build something slay with it ✨