Prerequisites Assumptions

To perform segmental duplication analysis of eukaryotic genomes, the reader needs access to a modest-sized cluster-computer or super-computer with a minimum of 4 GB of RAM available to each CPU (see Note 2) running any variant of a UNIX or Linux operating system (see Note 3). Competency in using UNIX command line utilities and programming in Perl is also a necessity (see Note 4). It is also a prerequisite that the BioPerl package (see Note 5) be available in the computing environment. Furthermore, the reader should be capable of using BioPerl to convert MegaBLAST alignment files into GFF records and should be familiar with the GFF version 3 specification (see Note 6).

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