phmmer

name	phmmer
description	Use when searching one or more protein query sequences against a protein sequence database with HMMER's one-pass sequence-vs-sequence searcher.
disable-model-invocation	true
user-invocable	true

phmmer

Quick Start

• Command: phmmer
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/phmmer
• Version: HMMER 3.4
• Full reference: See references/help.md

When To Use This Tool

• Search protein queries against a protein FASTA database without building a reusable profile HMM first.
• Use HMMER-style statistics for one-pass homolog discovery.
• Prefer jackhmmer when you want iterative family expansion, and hmmsearch when you already have a profile HMM.
• Use phmmer as a protein-oriented counterpart to nhmmer for nucleotide work.

Common Patterns

# 1) Standard protein-vs-protein search with parseable output tables
phmmer \
  --tblout hits.tbl \
  --domtblout domains.tbl \
  --cpu 8 \
  query.fa \
  proteome.fa

# 2) Save the accepted-hit alignment for later model building
phmmer \
  -A accepted_hits.sto \
  query.fa \
  proteome.fa

# 3) Emit Pfam-style table output when that downstream format is useful
phmmer \
  --pfamtblout pfam.tbl \
  query.fa \
  proteome.fa

Recommended Workflow

1. Start from protein queries and a protein target database in FASTA or another supported sequence format.
2. Save --tblout and --domtblout outputs so sequence-level and domain-level significance can be inspected separately.
3. If the first-pass search is promising, keep -A output for downstream hmmbuild or manual curation.
4. Escalate to jackhmmer if you need iterative sensitivity rather than a one-shot scan.

Guardrails

• In this workspace the binary currently fails to start because libopenblas.so.0 is missing.
• phmmer is for protein queries against protein sequence databases, not nucleotide targets.
• Positional argument order matters: query sequence file first, target database second.
• If your input is nucleotide, the HMMER family itself suggests using nhmmer or nhmmscan instead.