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What emerge installs as dependencies is affected by the USE flag-settings.They decide which optional features will be included when installing or upgrading an application.These are still installed with emerge, just by appending a "-bin" to the package name to instead install the binary version.Gentoo does have a binary packaging format, which is a .tbz2 file (tar with bzip2 compression) with additional metadata.Although the system itself is known as Portage, it consists of two main parts, the ebuild system and emerge.The ebuild system takes care of the actual work of building and installing packages, while emerge provides an interface to ebuild: managing an ebuild repository, resolving dependencies and similar issues.

A list of available USE flags is available at the Gentoo website's USE Flag Index.

(These two therefore have roughly the same relation as rpm has with yum, or dpkg has with APT.) A GTK -based GUI, Porthole, is available for working with Portage.

There is also the Himerge GUI, which stands for "Haskell Interface for e Merge".

For example, in packages which use a configure script, the USE flag .

The specification of USE flags is the usual way to configure programs on Gentoo.The program calculates and manages dependencies, executes ebuilds and maintains the local Portage tree and database of installed packages.