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 filename�
/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.