ClustalW - A multiple sequence alignment program
by Des Higgins and colleages.
PARAMETERS (set things)
***General settings:****
/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
***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.