1. A modest-sized cluster-computer or super-computer with 4 GB of RAM per CPU running any variant of a UNIX or Linux operating system.

2. Internet connection, ftp utilities (e.g., ftp, ncftp, wget).

3. Archiving utilities (e.g., unzip).

4. An assembled genome sequence of a eukaryotic organism that is lower case masked for repetitive elements.

5. The BLAST suite of programs (particularly formatdb and MegaBLAST).

6. Perl, BioPerl.

7. Approximately 5 to 20 GB of disk space to store sequence data, blast databases, alignment data, and parsed output.

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