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Programs written for a specific operating system generally must be run on that operating system; the OS provides "hooks" so each program doesn't have to reinvent the wheel. For example, Windows has a standard routine for displaying a dialog box, so every programmer that wants to show a dialog box doesn't have to write all those routines over again for each new program. However, Linux has its own built in routines which are different from those in Windows (or DOS, or other operating systems), so a Windows or DOS program generally won't work under Linux.

This is not exactly a "disadvantage of Linux," since the opposite is also true: Linux programs won't run under DOS or Windows. And since many Linux programs are free (as in "free beer") you can probably get a program that does what you want at no cost for Linux whereas you'd have to pay for a DOS or Windows program to do that. (However, since they're also usually free as in "free speech," a no-cost Windows version may also exist.)

The quality of these free programs does vary a bit, but many of them are arguably as good or better than the commercial programs costing hundreds of dollars.

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