Select the sequences to be aligned as usual ("Current Species", "Selected Species", "Marked Species").
Select a PT-Server to be used. Make sure it is up to date and contains all sequences you want to be considered as reference.
HINT: Unless you deselect the "Realign" button in the advanced menu, no sequence will be used as a reference for itself.
HINT: Sequences with less than 10 gaps are considered not aligned, and also not used as a reference.
Select a positional variability filter. If possible, use the filter appropriate for the type of sequences you want aligned. Positional variability statistics will be considered when placing the individual bases.
Decide what to do with possible overhang. If your sequence extends beyond the reference sequences on either side of the alignment, those bases cannot be aligned properly. Three options of handling this situation are supported:
just leave them dangling, directly attached to the last base that could be aligned properly
"move to edge"
move them out to the very beginning and end of the alignment. This allows you to easily spot sequences with overhang, and decide what to do yourself. Recommended, but only if you check your sequences after alignment!
automatically remove these bases.
Select a protection level higher than that of the sequences if you want the alignment software to actually modify the bases. Choose a lower protection level to execute a "dry run", not changing anything. Note that sequences with a protection level of zero will always be changed.
The Logging Level option allows you to change the noisiness of the alignment program. All output will be printed to the console from which you started ARB. The Option "debug_graph" may produce several large files for every sequence aligned and is not recommended for the uninitiated.