#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)
#SUB	subtopic.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		Export Column statistics to GnuPlot

OCCURRENCE	ARB_NT/SAI/Etc/Export Column statistics to GnuPlot

DESCRIPTION

        - Select a valid column statistic

        - Select what kind of information should be extracted

             Information         Formula
             -------------------------------------
             G+C ratio           (G+C) / N
             G+A ratio           (G+A) / N
             Rate                mutation_sum / frequency_sum
             TT ratio            (min.mutations + transversions) / transversions
             Most freq. base     F1 / N
             2nd freq. base      F2 / N
             3rd freq. base      F3 / N
             Least freq. base    F4 / N
             A ratio             A / N
             C ratio             C / N
             G ratio             G / N
             TU ratio            (T+U) / N
             Helix               boolean (helix or not helix)

             Legend:
             -------
             A/C/G/T/U = amount of A/C/G/T/U's in each column
             N         = total amount of bases in each column
             Fx        = F1 = count of most freq. base, ..., F4 of least freq. base


        - Select if you like smoothing of the values (before they are written to file)
          '1' means no smoothing, '2' means each value is smoothed with its neighbor, etc.
	  If you e.g. smooth by '21', then the statistic will contain 20 columns less than
	  the unsmoothed stat (for each 21-tupel only one value is written, i.e. 10 values are
	  missing on the left and 10 are missing on the right side).

        - Select a filter

        - Select a filename (specify without extension, which will be appended by ARB)

        - Press 'Save' to save to a file or
          Press 'Save & View' to save and start gnuplot

          In the last case you have some more options:

             - Select gnuplot-internal smoothing function

             - Select if to overlay other statistics (which were saved before)

NOTES           Pressing 'Delete all overlayed files' will delete all the files, which would be
                overlayed, if you press 'Save & View'.

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known