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
AUTHORS¶
Benjamin Redelings.