alignment-draw - Draw an alignment to HTML, optionally coloring residues by AU.

       Benjamin Redelings.

                                                    Feb 2018                                   alignment-draw(1)

       Draw an alignment to HTML, optionally coloring residues by AU.

       Rainbow+contrast+fade AA+contrast+fade+fade+fade+fade

-h, –help
              produce help message

       –filearg
              file with sequences and initial alignment

       –legend
              Print a legend showing how color-scheme indicates uncertainty.

       –show-ruler
              Print a ruler to show column numbers

       –column-colors
              Color-code column ticks by column certainty

       –AUarg
              file with alignment uncertainties

       –show-gapsarg (=yes)
              Show gaps

       –gaps-differentarg (=yes)
              Color gaps in grey.

       –widtharg
              The number of columns per line

       –startarg
              The first column to plot

       –endarg
              The last column to plot

       –formatarg (=HTML)
              produce a plot in this format

       –minarg
              Minimum value of scale function

       –maxarg
              Maximum value of scale function

       –color-schemearg
              Include a length of how certainties map to colors

       –scalearg (=LOD)
              scale for the uncertainties

alignment-draw - Draw an alignment to HTML, optionally coloring residues by AU.

       BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

       Please send bug reports to <bali-phy-users@googlegroups.com>.

alignment-drawalignment [AUfile] [OPTIONS]