Command line parameters

                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).
/CONVERT            :output the input sequences in a different file format.


        PARAMETERS (set things)
***General settings:****
/INTERACTIVE :read command line, then enter normal interactive menus
/QUICKTREE   :use FAST algorithm for the alignment 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)
/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 or filename
/PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename²
/PWGAPOPEN=f  :gap opening penalty        /PWGAPEXT=f  :gap extension penalty

***Multiple Alignments:***
/NEWTREE=    :file for new guide tree
/USETREE=    :file for old guide tree
/MATRIX=     :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
/DNAMATRIX=  :DNA weight matrix=IUB, CLUSTALW 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      :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
/NEWTREE1=    :file for new guide tree for profile1
/NEWTREE2=    :file for new guide tree for profile2
/USETREE1=    :file for old guide tree for profile1
/USETREE2=    :file for old guide tree for profile2

***Sequence to Profile Alignments:***
/SEQUENCES   :Sequentially add profile2 sequences to profile1 alignment
/NEWTREE=    :file for new guide tree
/USETREE=    :file for old guide tree

***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 

***Trees:***
/OUTPUTTREE=nj OR phylip OR dist
/SEED=n      :seed number for bootstraps.
/KIMURA      :use Kimura's correction.   /TOSSGAPS  :ignore positions with gaps.