| name | clustalw |
| description | Use when performing multiple sequence alignments on protein or nucleotide sequences, generating phylogenetic trees, or producing alignment output in various formats. |
| disable-model-invocation | true |
| user-invocable | true |
clustalw
Quick Start
- Command:
clustalw -infile=seqs.fa -align
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/clustalw
- Full reference: See
references/help.md
When To Use This Tool
- Build multiple sequence alignments for protein or nucleotide sequences.
- Generate CLUSTAL-style guide trees or distance trees as part of alignment workflows.
- Convert between alignment output formats such as CLUSTAL, FASTA, PHYLIP, NEXUS, and GCG.
- Merge alignments or add sequences with profile-alignment workflows.
Common Patterns
clustalw \
-infile=seqs.fa \
-align \
-outfile=seqs.aln \
-output=clustal
clustalw \
-infile=markers.fa \
-type=dna \
-align \
-tree \
-outputtree=phylip
clustalw \
-profile \
-profile1=alignment1.aln \
-profile2=alignment2.aln \
-outfile=merged.aln
Recommended Workflow
- Decide whether you are doing a fresh alignment, tree generation from an existing alignment, or profile alignment between two existing alignments.
- Set
-type=protein or -type=dna explicitly when auto-detection would be ambiguous.
- Run the alignment and inspect the emitted alignment file plus any guide-tree outputs such as
.dnd.
- If the downstream goal is rigorous phylogenetic inference, treat the CLUSTAL tree as a quick guide and move to a dedicated tree-inference tool afterward.
Guardrails
clustalw expects its classic long-option style such as -infile=...; bare GNU-style --help, --version, and -h are not valid help invocations.- Use
-help, -fullhelp, or -options to inspect available parameters.
- Do not run
clustalw with no arguments in automation; it can drop into its legacy interactive behavior instead of doing useful batch work.
- The tree output is primarily a guide/distance tree, not a substitute for model-based maximum-likelihood phylogeny.
