NAME

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

SYNOPSIS

       alignment-draw alignment [AU file] [OPTIONS]

DESCRIPTION

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

GENERAL OPTIONS:

       -h, –help
              produce help message

       –file arg
              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

       –AU arg
              file with alignment uncertainties

       –show-gaps arg (=yes)
              Show gaps

       –gaps-different arg (=yes)
              Color gaps in grey.

       –width arg
              The number of columns per line

       –start arg
              The first column to plot

       –end arg
              The last column to plot

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

       –min arg
              Minimum value of scale function

       –max arg
              Maximum value of scale function

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

       –scale arg (=LOD)
              scale for the uncertainties

EXAMPLES:

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

REPORTING BUGS:

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

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

AUTHORS

       Benjamin Redelings.

                                                    Feb 2018                                   alignment-draw(1)