Create an Overview Window. See "The Overview Window" for details.
Add a blank line separator just below the selected sequence. Be aware that only one sequence should be highlighted. Adding separator allow the user to create his own clusters.
Remove the separator just below the selected sequence. Be aware that only one sequence should be highlighted.
Remove unnecessary separators, unselect all.
Enter the Editor mode. The Editor is described in details in the "The Ordalie Alignment Editor" section
Display the secondary structures of all available PDB sequences. The secondary structure are taken from the PDB header. Alpha helices are desplayed in red, Pi helices in magenta, Beta strands in green and turns in cyan. This option is invoked by default when an alignment is loaded.
Hide the secondary structure information
Color sequeces names according to their phlylum information if available. Eukaryota are in red, Archae in blue, Bacteria in yellow.
Hide Phylum coloring