tRNAscan-SE was written in Perl. The implementation of the Pavesi algorithm [Pavesi et al., 1994], EufindtRNA, was written in C. A single package of the UNIX-based programs used by tRNAscan-SE is available at http://www.genetics.wustl.edu/eddy/software. All analysis times given are for a Silicon Graphics Indigo2 R4400 200 Mhz workstation. A web server is available for on-line tRNA analysis at http://www.genetics.wustl.edu/eddy/tRNAscan-SE/.