CLUSTAL 2.1 Multiple Sequence Alignments


clustalw option list:-
		-help 
		-fullhelp 
		-quiet 
		-check 
		-options 
		-align 
		-newtree=filename 
		-usetree=filename 
		-newtree1=filename 
		-usetree1=filename 
		-newtree2=filename 
		-usetree2=filename 
		-bootstrap 
		-tree 
		-quicktree 
		-convert 
		-interactive 
		-batch 
		-iteration=tree OR alignment OR none
		-infile=filename 
		-profile1=filename 
		-profile2=filename 
		-type=protein OR dna
		-profile 
		-sequences 
		-matrix=filename 
		-dnamatrix=filename 
		-negative 
		-noweights 
		-gapopen=f 
		-gapext=f 
		-endgaps 
		-nopgap 
		-nohgap 
		-novgap 
		-hgapresidues=string 
		-maxdiv=n 
		-gapdist=n 
		-pwmatrix=filename 
		-pwdnamatrix=filename 
		-pwgapopen=f 
		-pwgapext=f 
		-ktuple=n 
		-window=n 
		-pairgap=n 
		-topdiags=n 
		-score=percent OR absolute
		-transweight=f 
		-seed=n 
		-kimura 
		-tossgaps 
		-bootlabels=node OR branch
		-debug=n 
		-output=gcg OR gde OR pir OR phylip OR nexus OR fasta OR clustal
		-outputtree=nj OR phylip OR dist OR nexus
		-outfile=filename 
		-outorder=input OR aligned
		-case=lower OR upper
		-seqnos=off OR on
		-seqno_range=off OR on
		-range=string 
		-nosecstr1 
		-nosecstr2 
		-secstrout=structure OR mask OR both OR none
		-helixgap=n 
		-strandgap=n 
		-loopgap=n 
		-terminalgap=n 
		-helixendin=n 
		-helixendout=n 
		-strandendin=n 
		-strandendout=n 
		-numiter=n 
		-clustering=nj OR upgma
		-maxseqlen=n 
		-stats=filename 
		-pim