\begin{tabular}{ll}\hline
\Showoption{db}& specify database files (mandatory)
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\Showoption{q}& specify query files
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\Showoption{smap}& specify file containing a symbol mapping
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\Showoption{dna}& input is DNA sequence
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\Showoption{protein}& input is Protein sequence
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\Showoption{indexname}& specify name for index to be generated
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\Showoption{pl}& specify prefix length for bucket sort
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\Showoption{rev}& use reverse input sequence
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\Showoption{tis}& output transformed input sequences (tistab) to file
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\Showoption{ois}& output original input sequences (oistab) to file
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\Showoption{suf}& output suffix array (suftab) to file
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\Showoption{sti1}& output reduced inverse suffix array (sti1tab) to file
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\Showoption{bwt}& output Burrows-Wheeler Transformation (bwttab) to file
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\Showoption{bck}& output bucket boundaries (bcktab) to file
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\Showoption{lcp}& output longest common prefix lengths (lcptab) to file
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\Showoption{skp}& output skip values (skptab) to file
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\Showoption{allout}& output all index tables to files
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\Showoption{v}& verbose mode
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\Showoption{help}& this option
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\hline
\end{tabular}
