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:
- -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
EXAMPLES:
Rainbow+contrast+fade AA+contrast+fade+fade+fade+fade
REPORTING BUGS:
BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.