\begin{tabular}{ll}\hline
\Showoptiongroup{Input~parameter}
\Showoption{q}& specify files containing queries to be matched
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\Showoption{dnavsprot}& perform six frame translation of DNA
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\Showoptiongroup{Kind~of~matches}
\Showoption{tandem}& compute right branching tandem repeats
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\Showoption{supermax}& compute supermaximal matches
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\Showoption{mum}& compute maximal unique matches
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\Showoption{complete}& specify that query sequences must match completely
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\Showoptiongroup{Postprocessing~of~matches}
\Showoption{dbnomatch}& mask all database substrings containing a match
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\Showoption{qnomatch}& show all query substrings not containing a match
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\Showoption{dbmaskmatch}& mask all database substrings containing a match
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\Showoption{qmaskmatch}& mask all query substrings containing a match
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\Showoption{dbcluster}& cluster the database sequences
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\Showoption{nonredundant}& generate file with non-redundant set of sequences;
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\Showoption{pp}& generic postprocessing of matches
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\Showoption{selfun}& specify shared object file containing selection function
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\Showoptiongroup{Algorithms}
\Showoption{online}& run algorithms online without using the index
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\Showoption{qspeedup}& specify speedup level when matching queries
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\Showoptiongroup{Direction~of~matches}
\Showoption{d}& compute direct matches (default)
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\Showoption{p}& compute palindromic (i.e. reverse complemented matches)
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\Showoptiongroup{Match~constraints}
\Showoption{l}& specify that match must have the given length
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\Showoption{h}& specify the allowed hamming distance $\symbol{62}$ 0
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\Showoption{e}& specify the allowed edit distance $\symbol{62}$ 0
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\Showoption{allmax}& show all maximal matches in the order of their computation
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\Showoption{seedlength}& specify the seed length
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\Showoption{hxdrop}& specify the xdrop value for hamming distance extension
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\Showoption{exdrop}& specify the xdrop value for edit distance extension
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\Showoption{leastscore}& specify the minimum score of a match
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\Showoption{evalue}& specify the maximum E-value of a match
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\Showoption{identity}& specify minimum identity of match in range [1..100$\symbol{37}$]
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\Showoptiongroup{Output~modes}
\Showoption{sort}& sort the matches, additional argument is mode
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\Showoption{best}& show the best matches (those with smallest E-values)
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\Showoption{i}& give information about number of different matches
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\Showoptiongroup{Output~formats}
\Showoption{s}& show the alignment of matching sequences
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\Showoption{showdesc}& show sequence description of match
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\Showoption{f}& show filename where match occurs
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\Showoption{absolute}& show absolute positions
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\Showoption{nodist}& do not show distance of match
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\Showoption{noevalue}& do not show E-value of match
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\Showoption{noscore}& do not show score of match
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\Showoption{noidentity}& do not show identity of match
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\Showoptiongroup{Miscellaneous}
\Showoption{v}& verbose mode
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\Showoption{version}& show the version of the Vmatch package
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\Showoption{help}& show basic options
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\Showoption{help+}& show all options
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\hline
\end{tabular}
