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The difference : Hooks can not be removed or put offline (except if you make something inside apps for example) Hooks can not have option than you can activate (except if you make something inside apps for example) Hooks can display or make action on your website --> bootstrap is inside a hooks, it better that to include inside a header tag. Header_tag Yyou can choose if you want to put in header or footer You can activate or deactivate You can install or not You can make some different option There is more flexibility than a hooks? --> google analytics is better to be included inside header tag Which use ? Depend what you want to do. If you want to include some options, header tags is better. In summary