muscle

name	muscle
description	Use when performing multiple sequence alignment of FASTA inputs, generating alignment ensembles, or calculating alignment confidence metrics.
disable-model-invocation	true
user-invocable	true

muscle

Quick Start

• Command: muscle -align input.fa -output aln.afa
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/muscle
• Version: 5.3
• Full reference: See references/help.md

When To Use This Tool

• Align FASTA sequences with MUSCLE 5.
• Use -super5 for larger inputs when plain -align becomes too expensive.
• Generate alignment ensembles and confidence summaries, not just one alignment.
• Prefer MUSCLE when ensemble-based confidence analysis is part of the task.

Common Patterns

# 1) Standard alignment
muscle -align input.fa -output aln.afa

# 2) Large-input alignment with Super5
muscle -super5 input.fa -output aln.afa

# 3) Generate a stratified ensemble
muscle -align input.fa -stratified -output ensemble.efa

# 4) Extract the highest-confidence replicate
muscle -maxcc ensemble.efa -output maxcc.afa

Recommended Workflow

1. Start with -align for ordinary datasets.
2. Switch to -super5 when sequence count makes ordinary alignment too slow or memory-heavy.
3. If alignment confidence matters, generate an ensemble and summarize it rather than trusting one run.
4. Inspect the final alignment before phylogeny or profile construction.

Guardrails

• -super5 is the recommended path for larger inputs.
• Input is FASTA; output is usually aligned FASTA or EFA depending on the mode.
• -super5 does not directly emit EFA output.
• Ensemble workflows are more informative, but they also produce more files and more interpretation work.