<p>Abstract</p> <p>Background</p> <p>Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using <it>SNaPshot</it>, a primer-extension-based method, a multiplex of 25 SNPs in a single reaction has been practiced for reducing the expense of genotyping a panel of SNPs useful for identity control.</p> <p>Findings</p> <p>To further decrease <it>SNaPshot</it>'s cost, we introduced the Perl script <it>SNPmplexViewer</it>, which facilitates the analysis of trace files for reactions performed without the use of fluorescent size standards. <it>SNPmplexViewer </it>automatically aligns reference and target trace electropherograms, run with and without fluorescent size standards, respectively. <it>SNPmplexViewer </it>produces a modified target trace file containing a normalised trace in which the reference size standards are embedded. <it>SNPmplexViewer </it>also outputs aligned images of the two electropherograms together with a difference profile.</p> <p>Conclusions</p> <p>Modified trace files generated by <it>SNPmplexViewer </it>enable genotyping of <it>SnaPshot </it>reactions performed without fluorescent size standards, using common fragment-sizing software packages. <it>SNPmplexViewer</it>'s normalised output may also improve the genotyping software's performance. Thus, <it>SNPmplexViewer </it>is a general free tool enabling the reduction of <it>SNaPshot</it>'s cost as well as the fast viewing and comparing of trace electropherograms for fragment analysis. <it>SNPmplexViewer </it>is available at <url>http://cowry.agri.huji.ac.il/cgi-bin/SNPmplexViewer.cgi</url>.</p
