alignment-draw(1)

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.