NAME

       chain2dim - two-dimensional match chaining

SYNOPSIS

       chain2dim [options] <matchfile>

OPTIONS

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

       -local <param>
           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.

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

       -maxgap <width>
           Maximal width of gap in chain.

       -outprefix <prefix>
           Specify prefix of files to output chains.

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

       -thread <keywords...>
           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.

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

       -v
           Be verbose.

       -version
           Show the version of the Vmatch package.

       -help
           Show help.

SEE ALSO

       vmatch(1)

                                                                                                    CHAIN2DIM(1)