Native files are the file formats used within page layout and word processing applications when saving a said document. For instance a file saved from Microsoft PowerPoint would have a ".ppt" extension (MyFileName.ppt) and this is generically considered a native file format (as compared to exporting, ripping or distilling to PDF, ps or EPS, which are PostScript type files and more difficult to edit without special tools or software.). Native file formats allow an application to distinguish the type of file and how to handle it. Generally speaking the native file formats can not be easily interchanged without conversion software. Native files are generally more editable within their source application, although with the advent of XML, this is slowly changing.
Common printing specific native file formats include:
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.qxp - QuarkXPress (versions 6 and 7)
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.qxd - QuarkXPress (versions 3, 4 and 5)
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.ind - Adobe InDesign (all versions, CS1, CS2, etc.)
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.ai - Adobe Illustrator
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.psd - Adobe PhotoShop
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.doc - Microsoft Office Document