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Background  There is a need for software scripts and modules for format parsing, data manipulation, statistical analysis and annotation especially for tasks related to marker identification from sequence data and sequence diversity analysis.    Results  Here we present several new Perl scripts and a module for sequence data diversity analysis. To enable the use of these software with other public domain tools, we also make available PISE (Pasteur Institute Software Environment) wrappers for these Perl scripts and module. This enables the user to generate pipelines for automated analysis, since PISE is a web interface generator for bioinformatics programmes.    Conclusion  A new set of modules and scripts for diversity statistic calculation, format parsing and data manipulation are available with PISE wrappers that enable pipelining of these scripts with commonly used contig assembly and sequence feature prediction software, to answer specific sequence diversity related questions.

Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features