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 paramters
/HELP or /CHECK :outline the command line params.
/ALIGN :do full multiple alignment
/PROFILE :merge two alignments (PROFILE1 and 2) by profile alignment
/SEQUENCES :sequentially add PROFILE2 sequences to PROFILE1 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, MD, ID or filename
/PWGAPOPEN=f :gap opening penalty /PWGAPEXT=f :gap opening penalty
***Multiple Alignments:***
/MATRIX= :BLOSUM, PAM, MD, 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
/NOPGAP :Pascarella 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.