This is the command gt-chain2dim that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 <[email protected]>.
Use gt-chain2dim online using onworks.net services
