GT-CHAIN2DIM(1)

NAME
gt-chain2dim - Chain pairwise matches.

SYNOPSIS

gt chain2dim [options] -m matchfile

OPTIONS

-m
    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
    specify weight factor > 0.0 to obtain score of a fragment requires one of the options -local const -global gc -global ov (default: 1.00)

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

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

-v
    be verbose (default: no)

-help
    display help and exit

-version
    display version information and exit

AUTHOR

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