This distribution includes the PERL script tRNAscan-SE, all the files necessary to compile and run the complete COVE package (version 2.4.4), all the files necessary to compile and run the modified version of tRNAscan (version 1.4), and all the files needed to compile and run EufindtRNA 1.0 (the cove programs, tRNAscan 1.4, and EufindtRNA are included for use with the tRNAscan-SE program, but may also be run as stand-alone programs). Installation of the PERL (Practical Extraction and Report Language, Larry Wall) interpreter package version 5.0 or later is required to run the tRNAscan-SE PERL script.