Set basic options for the parsimony program. If you do not want to use a filter, you should select a filter (eg. E. coli) which excludes only the big gaps in the alignment. Otherwise the program will count thousands of uninformative columns. If you want a transversion parsimony, open the filter window, and change the "simplify" option to TRANSVERSIONS ONLY
After pressing go, no species is added, no tree is changed, you only get a new window (with some action buttons).
You can only change filter settings at start-up time. You should use filters in combination with large databases to speed up computation. Gaps ('-') are treated as bases, so check for gaps at the beginning or end of short sequences. Replace them by '.'.
All sequences are read at start-up time. Sequence changes afterwards are ignored. Restart arb_parsimony if you want them to take effect.