Global chaining. Optional parameter "gc" switches on gap costs (according to L1-model). Optional parameter "ov" means that overlaps between matches are allowed.

Compute local chains (according to L1-model). If no parameter is given, compute local chains with maximum score. If parameter is given, this must be a positive number optionally followed by the character b or p. If only the number, say k, is given, this is the minimum score of the chains output. If a number is followed by character b, then output all chains with the largest k scores. If a number is followed by character p, then output all chains with scores at most k percent away from the best score.

Specify weight factor > 0.0 to obtain the score of a fragment. Requires one of the options -local, -global gc or -global ov.

Maximal width of gap in chain.

Specify prefix of files to output chains.

Only compute chains which do not cross sequence borders (not possible for matches in open format).

Thread the chains, i.e. close the gaps. Accepts an optional list of keywords "minlen1 minlen2 maxerror1 maxerror2", each followed by a number specifies the minimum length and the maximum error rate of thread. 1 refers to match instance in indexed sequence, 2 refers to matching instance in query.

Do not output the chains and only report their lengths and scores.

Be verbose.

Show the version of the Vmatch package.

Show help.