Clustalw2

# 2) Run a standard multiple alignment
clustalw2 -INFILE=seqs.fa -ALIGN

# 3) Calculate a tree from an existing alignment
clustalw2 -INFILE=aligned.aln -TREE

Recommended Workflow

1. Prefer noninteractive flags such as -INFILE=... and -ALIGN for reproducible runs.
2. Use -HELP or -FULLHELP to review the older option syntax before launching a large job.
3. Set output-related flags deliberately if you do not want the default CLUSTAL alignment output.
4. Use the interactive mode only when you actually want menu-driven operation.

Guardrails

• -h and --help are not valid help flags here; they produce unknown-option errors.
• A bare clustalw2 invocation enters the interactive menu and waits for choices.
• This CLI uses legacy uppercase single-dash options such as -INFILE=..., -ALIGN, -TREE, -OUTPUT=....
• Default output format is CLUSTAL unless you override it with -OUTPUT=.
• The local build reports itself as CLUSTAL 2.1.