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.