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:

--help
produce help message
--align arg
file with sequences and initial alignment
--alphabet arg
Set to 'Codons' to prefer codon alphabets
--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.