CLUSTAL W(1.4) Multiple Sequence Alignments DATA (sequences) /INFILE=file.ext :input sequences. /PROFILE1=file.ext and /PROFILE2=file.ext :profiles (old alignment). VERBS (do things) /OPTIONS :list the command line parameters /HELP or /CHECK :outline the command line params. /ALIGN :do full multiple alignment /TREE :calculate NJ tree. /BOOTSTRAP(=n) :bootstrap a NJ tree (n= number of bootstraps; def. = 1000). PARAMETERS (set things) ***General settings:**** /INTERACTIVE :read command line, then enter normal interactive menus /QUICKTREE :use FAST algorithm for the alignment guide tree /NEWTREE= :file for new guide tree /USETREE= :file for old guide tree /NEGATIVE :protein alignment with negative values in matrix /OUTFILE= :sequence alignment file name /OUTPUT= :GCG, GDE, PHYLIP or PIR /OUTORDER= :INPUT or ALIGNED /CASE :LOWER or UPPER (for GDE output only) ***Fast Pairwise Alignments:*** /KTUP=n :word size /TOPDIAGS=n :number of best diags. /WINDOW=n :window around best diags. /PAIRGAP=n :gap penalty /SCORE :PERCENT or ABSOLUTE ***Slow Pairwise Alignments:*** /PWMATRIX= :BLOSUM, PAM, ID or filename /PWGAPOPEN=f :gap opening penalty /PWGAPEXT=f :gap opening penalty ***Multiple Alignments:*** /MATRIX= :BLOSUM, PAM, ID or filename /GAPOPEN=f :gap opening penalty /GAPEXT=f :gap extension penalty /ENDGAPS :no end gap separation pen. /GAPDIST=n :gap separation pen. range /NORGAP :Residue specific gaps off /NOHGAP :hydrophilic gaps off /HGAPRESIDUES= :list hydrophilic res. /MAXDIV=n :% ident. for delay /TYPE= :PROTEIN or DNA /TRANSITIONS :transitions NOT weighted. ***Trees:*** /SEED=n :seed number for bootstraps. /KIMURA :use Kimura's correction. /TOSSGAPS :ignore positions with gaps. clustalw option list:- /help /check /options /infile=filename /profile1=filename /profile2=filename /align /newtree=filename /usetree=filename /bootstrap /tree /quicktree /interactive /type=protein OR dna /matrix=filename /negative /gapopen=f /gapext=f /endgaps /norgap /nohgap /hgapresidues=string /maxdiv=n /gapdist=n /pwmatrix=filename /pwgapopen=f /pwgapext=f /ktuple=n /window=n /pairgap=n /topdiags=n /score=percent OR absolute /transitions /seed=n /kimura /tossgaps /debug=n /output=gcg OR gde OR pir OR phylip /outputtree=nj OR phylip OR dist /outfile=filename /outorder=input OR aligned /case=lower OR upper