| The ClustalW options are summarized in Tables Table 9-1 through Table 9-10. Table 9-1. ClustalW verb options | Option | Definition | | -align | Do full multiple alignment. | | -bootstrap(=n) | Bootstrap a NJ tree (n= number of bootstraps; def. = 1000). | | -convert | Output the input sequences in a different file format. | | -help or -check | Outline the command-line parameters | | -options | List the command-line parameters. | | -tree | Calculate NJ tree. | Table 9-2. ClustalW data options | Option | Definition | | -infile=file.ext | Input sequences. | | -profile1=file.ext | Profiles. | | -profile2=file.ext | Profiles (old alignment). | Table 9-3. ClustalW parameters general settings | Option | Definition | | -case | LOWER or UPPER (for GDE output only). | | -interactive | Read command line, then enter normal interactive menus. | | -negative | Protein alignment with negative values in matrix. | | -outfile= | Sequence alignment file name. | | -output= | GCG, GDE, PHYLIP, or PIR. | | -outorder= | INPUT or ALIGNED. | | -quicktree | Use FAST algorithm for the alignment guide tree. | | -seqnos= | OFF or ON (for ClustalW output only). | Table 9-4. ClustalW parameters fast pairwise alignments | Option | Definition | | -ktuple=n | Word size. | | -pairgap=n | Gap penalty. | | -score | PERCENT or ABSOLUTE. | | -topdiags=n | Number of best diags. | | -window=n | Window around best diags. | Table 9-5. ClustalW parameters slow pairwise alignments | Option | Definition | | -pwdnamatrix= | DNA weight matrix=IUB, ClustalW, or filename. | | -pwgapopen=f | Gap opening penalty. | | -pwgapext=f | Gap extension penalty. | | -pwmatrix= | Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename. | Table 9-6. ClustalW parameters multiple alignments | Option | Definition | | -dnamatrix= | DNA weight matrix=IUB, ClustalW, or filename. | | -endgaps | No end gap separation penalty. | | -gapdist=n | Gap separation penalty range. | | -gapext=f | Gap extension penalty. | | -gapopen=f | Gap opening penalty. | | -hgapresidues= | List hydrophilic residue. | | -matrix= | Protein weight matrix=BLOSUM, PAM, GONNET, ID, or filename. | | -maxdiv=n | Percentage identity for delay. | | -newtree= | File for new guide tree. | | -nohgap | Hydrophilic gaps off. | | -nopgap | Residue-specific gaps off. | | -transweight | Transitions weighted. | | -type= | PROTEIN or DNA. | | -usetree= | File for old guide tree. | Table 9-7. ClustalW parameters profile alignments | Option | Definition | | -newtree1= | File for new guide tree for profile1. | | -newtree2= | File for new guide tree for profile2. | | -profile | Merge two alignments by profile alignment. | | -usetree1= | File for old guide tree for profile1. | | -usetree2= | File for old guide tree for profile2. | Table 9-8. ClustalW parameters sequence to profile alignments | Option | Definition | | -newtree= | File for new guide tree. | | -sequences | Sequentially add profile2 sequences to profile1 alignment. | | -usetree= | File for old guide tree. | Table 9-9. ClustalW parameters structure alignments | Option | Definition | | -helixendin=n | Number of residues inside helix to be treated as terminal. | | -helixgap=n | Gap penalty for helix core residues. | | -helixendout=n | Number of residues outside helix to be treated as terminal. | | -loopgap=n | Gap penalty for loop regions. | | -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. | | -strandgap=n | Gap penalty for strand core residues. | | -strandendin=n | Number of residues inside strand to be treated as terminal. | | -strandendout=n | Number of residues outside strand to be treated as terminal. | | -terminalgap=n | Gap penalty for structure termini. | Table 9-10. ClustalW parameters trees | Option | Definition | | -kimura | Use Kimura's correction. | | -outputtree= | nj OR phylip OR dist. | | -seed=n | Seed number for bootstraps. | | -tossgaps | Ignore positions with gaps | |