hmmalign

name	hmmalign
description	Use when aligning sequences to a profile HMM to produce multiple sequence alignments.
disable-model-invocation	true
user-invocable	true

hmmalign

Quick Start

• Command: hmmalign [options] <hmmfile> <seqfile>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hmmalign
• Version: HMMER 3.4
• Full reference: See references/help.md

When To Use This Tool

• Add sequences to an existing HMM-guided alignment.
• Produce a multiple sequence alignment constrained by match states in a profile HMM.
• Recreate an alignment in Stockholm, Pfam, A2M, or PSIBLAST-compatible formats.
• Prefer hmmbuild when creating a model from an alignment instead of aligning new sequences to an existing one.

Common Patterns

# 1) Align sequences to a profile HMM and write Stockholm output
hmmalign \
  -o aligned.sto \
  profile.hmm \
  sequences.fa

# 2) Preserve the original seed alignment columns when mapping new sequences
hmmalign \
  --mapali seed_alignment.sto \
  -o mapped.sto \
  profile.hmm \
  new_sequences.fa

# 3) Trim terminal unaligned tails and emit A2M output
hmmalign \
  --trim \
  --outformat A2M \
  -o aligned.a2m \
  profile.hmm \
  sequences.fa

Recommended Workflow

1. Start from a trusted HMM built from a compatible alphabet and a sequence file in FASTA or another supported format.
2. Decide whether you need raw alignment output, mapped seed columns via --mapali, or trimmed termini via --trim.
3. Write the alignment explicitly with -o and set --outformat when downstream tools do not want Stockholm.
4. Review the aligned output before feeding it into phylogeny, consensus calling, or model rebuilding.

Guardrails

• Positional argument order matters: HMM first, sequence file second.
• The default output format is Stockholm written to stdout unless -o is used.
• Use -h for help; --help and --version are not accepted here.
• If alphabet autodetection is ambiguous, force it with --amino, --dna, or --rna, and use --informat when sequence parsing is the problem.