New sequence -- append a new, blank sequence to the sequence document.
Edit -- open single sequence editting view for selected items.
Reverse, Complement, Rev-complement -- Reverse, complement or reverse+complement a sequence. Works on one or more sequences, and the selected subrange.
Rna-Dna,Dna-Rna -- Convert dna to rna (t->u) and vice versa. Works on one or more sequences, and the selected subrange.
Degap -- remove alignment gaps "~". Works on one or more sequences, and the selected subrange. Gaps of "-" are locked and not affected by Degap. Works on one or more sequences, and the selected subrange.
Lock Indel & Unlock Indel -- Convert from unlocked gaps "~", to locked gaps "-". Unlocked gaps will disappear and appear as needed as you slide bases left and right. Locked gaps are not affected by sliding nor by Degap. Works on one or more sequences, and the selected subrange.
Consensus -- generate a consensus sequence of the selected sequences.
Translate -- translate to/from amino acid. Relies on Codon.Table data.
Pretty print -- a prettier view of a single or aligned sequences. Use these views to print your sequences. Printing from the editing display will not be supported fully, and may not print all of your sequence(s).
Restriction map -- Restriction enzyme cut points of selected sequence. Also protein translation options.
Dotty plot -- provide a dot plot comparison of two sequences.
Nucleic, amino codes -- These provide both reminders of the base codes, and a way to select colors to assocate with each code (new in v 1.9a). See below for some discussion of the two "aa-color" documents that now ship with SeqPup.