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CLUSTALW PARAMETERS

***General settings:****
-QUICKTREE   :use FAST algorithm for the alignment guide tree
-NEGATIVE    :protein alignment with negative values in matrix
-OUTORDER=   :INPUT or ALIGNED
-SEQNOS=     :OFF or ON (for Clustal output only)

***Fast Pairwise Alignments:***
-KTUPLE=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=    :Protein weight matrix=BLOSUM, PAM, GONNET, ID 
-PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW 
-PWGAPOPEN=f  :gap opening penalty        
-PWGAPEXT=f  :gap extension penalty

***Multiple Alignments:***
-MATRIX=     :Protein weight matrix=BLOSUM, PAM, GONNET, ID 
-DNAMATRIX=  :DNA weight matrix=IUB, CLUSTALW 
-GAPOPEN=f   :gap opening penalty             
-GAPEXT=f    :gap extension penalty
-ENDGAPS     :no end gap separation pen      
-GAPDIST=n   :gap separation pen. range
-NOPGAP      :residue-specific gaps off        
-NOHGAP      :hydrophilic gaps off
-HGAPRESIDUES= :list hydrophilic res    
-MAXDIV=n    :% ident. for delay
-TYPE=       :PROTEIN or DNA             
-TRANSWEIGHT :transitions weighted.

 ***Profile Alignments:***
-PROFILE     :Merge two alignments by profile alignment

***Sequence to Profile Alignments:***
-SEQUENCES   :Sequentially add profile2 sequences to profile1 alignment

***Structure Alignments:***
-NOSECSTR1     :do not use secondary structure-gap penalty mask for profile 1 
-NOSECSTR2     :do not use secondary structure-gap penalty mask for profile 2
-SECSTROUT=    :STRUCTURE or MASK or BOTH or NONE  output in alignment file
-HELIXGAP=n    :gap penalty for helix core residues 
-STRANDGAP=n   :gap penalty for strand core residues
-LOOPGAP=n     :gap penalty for loop regions
-TERMINALGAP=n :gap penalty for structure termini
-HELIXENDIN=n  :number of residues inside helix to be treated as terminal
-HELIXENDOUT=n :number of residues outside helix to be treated as terminal
-STRANDENDIN=n :number of residues inside strand to be treated as terminal
-STRANDENDOUT=n:number of residues outside strand to be treated as terminal