ClustalW - A multiple sequence alignment program by Des Higgins and colleages.
Program options:

do full multiple alignment

calculate NJ tree

use FAST algorithm for the alignment guide tree

Bootstrap NJ tree. (# boostraps)

Other options: 

                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.