ClustalW

ClustalW for multiple sequence alignment.

Command Line Usage

# Basic alignment
clustalw2 -INFILE=sequences.fasta -OUTFILE=aligned.fasta -OUTPUT=FASTA

# Protein alignment with specific parameters
clustalw2 -INFILE=proteins.fasta -TYPE=PROTEIN -OUTFILE=aligned.aln

# DNA alignment
clustalw2 -INFILE=dna.fasta -TYPE=DNA -OUTFILE=aligned.fasta -OUTPUT=FASTA

Output Formats

# FASTA output
clustalw2 -INFILE=seq.fasta -OUTPUT=FASTA -OUTFILE=aligned.fasta

# Clustal format
clustalw2 -INFILE=seq.fasta -OUTPUT=CLUSTAL -OUTFILE=aligned.aln

# PHYLIP format
clustalw2 -INFILE=seq.fasta -OUTPUT=PHYLIP -OUTFILE=aligned.phy

# GCG/MSF format
clustalw2 -INFILE=seq.fasta -OUTPUT=GCG -OUTFILE=aligned.msf

BioPython Integration

from Bio.Align.Applications import ClustalwCommandline
from Bio import AlignIO

# Run ClustalW
clustalw_cline = ClustalwCommandline("clustalw2",
                                      infile="sequences.fasta",
                                      outfile="aligned.aln")
stdout, stderr = clustalw_cline()

# Read alignment
alignment = AlignIO.read("aligned.aln", "clustal")
print(f"Alignment length: {alignment.get_alignment_length()}")

Guide Tree

# Generate guide tree only
clustalw2 -INFILE=sequences.fasta -TREE -OUTPUTTREE=phylip

# Use existing guide tree
clustalw2 -INFILE=sequences.fasta -USETREE=guide_tree.dnd