Clustalw

# 2) Align DNA sequences and write a PHYLIP tree
clustalw \
  -infile=markers.fa \
  -type=dna \
  -align \
  -tree \
  -outputtree=phylip

# 3) Merge two existing alignments by profile alignment
clustalw \
  -profile \
  -profile1=alignment1.aln \
  -profile2=alignment2.aln \
  -outfile=merged.aln

Recommended Workflow

1. Decide whether you are doing a fresh alignment, tree generation from an existing alignment, or profile alignment between two existing alignments.
2. Set -type=protein or -type=dna explicitly when auto-detection would be ambiguous.
3. Run the alignment and inspect the emitted alignment file plus any guide-tree outputs such as .dnd.
4. 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.