gt-chain2dim - Chain pairwise matches.


gt chain2dim [options] -m matchfile


-m [filename]

Specify file containing the matches mandatory option (default: undefined)


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


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)


display help and exit


display version information and exit


Report bugs to <>.