alignment-draw - Draw an alignment to HTML, optionally
coloring residues by AU.
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
- –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>.
Please send bug reports to
<bali-phy-users@googlegroups.com>.