$res = exec('C:\\clustalw2 -INFILE=seq.fasta -ALIGN -TYPE=Protein -ktuple=1 -window=5 -score=percent -topdiags=5 -pairgap=3 -pwmatrix=gonnet -pwdnamatrix=iub -pwgapopen=10 -pwgapext=0.1 -matrix=gonnet -dnamatrix=iub -gapopen=10 -gapext=0.2 -gapdist=5 -iteration=none -numiter=1 -clustering=NJ -seqnos=on -outorder=aligned -OUTFILE=res.aln',$out);
print_r($out);

This code runs just fine. But the problem i'm facing is that the clustalw2 is performing only pairwise sequence alignment and not multiple sequence alignment eventhough my file has more than 2 sequences. Where m i goin wrong? Can any one please help!