Mummerplot is a perl script that generates gnuplot scripts and data collections for plotting with the gnuplot utility. It can generate 2-d dotplots and 1-d coverage plots for the output of mummer or nucmer. It can also color dotplots with an identity color gradient.
Options::
-b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end -color Color plot lines with a percent similarity gradient or turn off all plot color (default color by match dir) If the plot is very sparse, edit the .gp script to plot with 'linespoints' instead of 'lines' -c Generate a reference coverage plot (default for .tiling) --filter Only display .delta alignments which represent the "best" hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences --fat Layout sequences using fattest alignment only -IdR Plot a particular reference sequence ID on the X-axis -IdQ Plot a particular query sequence ID on the Y-axis -s Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small') --SNP Highlight SNP locations in each alignment -title Specify the gnuplot plot title (default none) -x Set the xrange for the plot '[min:max]' -y Set the yrange for the plot '[min:max]' -R Plot an ordered set of reference sequences from Rfile -Q Plot an ordered set of query sequences from Qfile --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options