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alignment-draw(1) 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:

produce help message
file with sequences and initial alignment
Print a legend showing how color-scheme indicates uncertainty.
Print a ruler to show column numbers
Color-code column ticks by column certainty
file with alignment uncertainties
Show gaps
Color gaps in grey.
The number of columns per line
The first column to plot
The last column to plot
produce a plot in this format
Minimum value of scale function
Maximum value of scale function
Include a length of how certainties map to colors
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