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Mummerplot (version 4.0.0rc1+galaxy2)
Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)
Color plot lines with a percent similarity gradient or turn off all plot color.
Generate a reference coverage plot (default for .tiling) or the defualt dotplot.
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. (--filter)
(--fat)
For alignments that used more than one reference/query.
Set the output size to small, medium or large. (-s)
Highlight SNP locations in each alignment. (--SNP)
(-title)

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.

Outputs:
  • gnuplot: The gnuplot script
  • fplot, rplot, hplot: The forward, reverse, and highlighted match information for plotting with gnuplot.
  • plot: The plotted image file

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