| -pair | Align a pair of sequences (first two in input file). |
| -nogaps | Strip gaps from input sequences. |
| -consolidategaps | Remove positions in alignment with only gaps. |
| -identity | Pairwise identity. |
| -similarity 0.5 | Pairwise similarity: threshold for counting similar residues (default 0.5). |
| -profile | Generate a profile from an alignment. |
| -information | Information analysis. |
| -hydrophobicity 0.8 | Hydrophobicity analysis: representation threshold (fraction of # of seqs). |
| -select 3,0.85 | Select relative to a reference sequence and cutoff. |
| -length 128,435 | Select sequences within a length range. |
| -delete | Delete non-selected sequences. |
| -verbose 7 | Verbosity of output. |
| -gap 10,0.2 | Gap opening and extending penalties for alignment (default 20,0.2). |
| -segments 1-33,36-69 | Selection of sequence segments (default all). |
| Every pair of numbers indicate a segment to select. | |
| -sequences 2,18 | Subset of sequences to compare (default all). |
| -window 17 | Window for moving averages (default 20). |
| -properties file.star | Property file (default = internal values). |
| -Similarity sim.star | Residue similarity matrix (default blosum62.star). |
| -Matrix file.mat | Matrix output filename. |
| -Image file.img | Image output filename. |
| -Postscript file.ps | Postscript output filename. |