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.