N.B. these lists include general-purpose StockholmFormat utilities and not the heavyweight probabilistic modeling tools in DART, many of which use Stockholm as their native alignment format (see in particular PhyloGram.pm and xrate).
Standalone Perl scripts:
Visualization/colorization/pretty-printing of Stockholm alignments:
colorstock.pl - color alignment columns by stem in a Stockholm alignment of RNA secondary structures, using ANSI terminal color
constock.pl - given a database of Stockholm multiple alignments, all containing exactly the same sequences, return the "consensus" alignment (specifically, the subset of columns that maximises either the SumOfPairsScore or TotalColumnScore)
stockholm2ct.pl - extract secondary structures from a Stockholm alignment of RNA and write them as CT files (MFOLD)
cmpalign.cc and cmpfold.cc - benchmarking tools for finding the homology overlap between Stockholm alignments (in terms of the SumOfPairsScore) as well as the overlap of basepair annotations in RNA secondary structures
gc2gr-ss.cc - maps #=GC SS_cons lines (consensus secondary structure) to #=GR SS lines (by-sequence secondary structure)