NAME

       gt-chain2dim - Chain pairwise matches.

SYNOPSIS

       gt chain2dim [options] -m matchfile

DESCRIPTION

       -m [filename]
           Specify file containing the matches mandatory option (default: undefined)

       -global
           perform global chaining

           •   optional parameter gc switches on gap costs (according to L1-model)

           •   optional parameter ov means that overlaps between matches are allowed

           •   optional parameter all means that all optimal chains are processed

       -local
           perform local chaining compute local chains (according to L1-model).

           •   If no parameter is given, compute local chains with maximums 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 [value]
           specify weight factor > 0.0 to obtain score of a fragment requires one of the options
           -local const -global gc -global ov (default: 1.000000)

       -maxgap [value]
           specify maximal width of gap in chain (default: 0)

       -silent [yes|no]
           do not output the chains but only report their lengths and scores (default: no)

       -v [yes|no]
           be verbose (default: no)

       -help
           display help and exit

       -version
           display version information and exit

REPORTING BUGS

       Report bugs to <kurtz@zbh.uni-hamburg.de>.