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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 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