alignment-draw(1)

Usage

alignment-draw alignment [AU file] [OPTIONS]

Draw an alignment to HTML, optionally coloring residues by AU.

`-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
`–show-letters arg (=yes)`	Show letters
`–show-names arg (=yes)`	Show names
`–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

Rainbow+contrast+fade AA+contrast+fade+fade+fade+fade

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .

4 releases since Debian 10 (Buster); the text changed 2 times.