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