Method                          Scripts
                Queries without flanks          Queries with flanks
--------------------------------------------------------------------
Probalign       do_probalignRNA4.pl             do_probalignRNA.pl
BLAST           do_blast3_gengen.pl             do_blast3.pl
SSEARCH         do_ssearch3_gengen.pl           do_ssearch3.pl
ClustalW        do_clustalw_gengen.pl           do_clustalw.pl
HMMER           NONE                            do_hmmer4.pl

Each script takes in the directory name of the benchmark and an optional
file suffix for multiple simultaneous runs. So if you want to run
Probalign on the benchmark without query flanks type

"perl do_probalignRNA.pl RNA-genome-only-divergent/"

Make sure the executables are present in the current directory.